<!DOCTYPE map PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp Map Version 1.0//EN" "http://java.sun.com/products/javahelp/map_1_0.dtd">\r
<map version="1.0">\r
<mapID target="home" url="html/index.html" />\r
+ <mapID target="start" url="html/start.html"/>\r
\r
- <mapID target="calculate" url="html/menus/calculateMenu.html" />\r
+ <mapID target="new" url="html/whatsNew.html"/>\r
+ <mapID target="search" url="html/features/search.html"/>\r
+ <mapID target="wrap" url="html/features/wrap.html"/>\r
+ <mapID target="overview" url="html/features/overview.html"/>\r
+ <mapID target="seqfeatures" url="html/features/seqfeatures.html"/>\r
\r
- <mapID target="colours" url="html/colourSchemes/colourSchemes.html" />\r
- <mapID target="colours.zappo" url="html/colourSchemes/colourSchemes.html#zappo" />\r
- <mapID target="colours.taylor" url="html/colourSchemes/colourSchemes.html#taylor" />\r
- <mapID target="colours.hydro" url="html/colourSchemes/colourSchemes.html#hydrophobic" />\r
- <mapID target="colours.helix" url="html/colourSchemes/colourSchemes.html#helix" />\r
- <mapID target="colours.strand" url="html/colourSchemes/colourSchemes.html#strand" />\r
- <mapID target="colours.turn" url="html/colourSchemes/colourSchemes.html#turn" />\r
- <mapID target="colours.buried" url="html/colourSchemes/colourSchemes.html#buried" />\r
- <mapID target="colours.nucleotide" url="html/colourSchemes/colourSchemes.html#nucleotide" />\r
- <mapID target="colours.blosum" url="html/colourSchemes/colourSchemes.html#blosum" />\r
- <mapID target="colours.pid" url="html/colourSchemes/colourSchemes.html#pid" />\r
+ <mapID target="webservice" url="html/webServices/index.html"/>\r
+ <mapID target="clustal" url="html/webServices/clustal.html"/>\r
+ \r
+ <mapID target="io" url="html/io/index.html"/>\r
+ <mapID target="edit" url="html/editing/index.html"/>\r
+ \r
+ <mapID target="trees" url="html/calculations/tree.html"/>\r
+ <mapID target="conservation" url="html/calculations/conservation.html"/> \r
+ <mapID target="pca" url="html/calculations/pca.html"/>\r
+ <mapID target="pairwise" url="html/calculations/pairwise.html"/>\r
+ <mapID target="redundancy" url="html/calculations/redundancy.html"/>\r
+ \r
+ <mapID target="colours" url="html/colourSchemes/index.html" />\r
+ <mapID target="colours.clustal" url="html/colourSchemes/clustal.html"/>\r
+ <mapID target="colours.zappo" url="html/colourSchemes/zappo.html" />\r
+ <mapID target="colours.taylor" url="html/colourSchemes/taylor.html" />\r
+ <mapID target="colours.hydro" url="html/colourSchemes/hydrophobic.html" />\r
+ <mapID target="colours.helix" url="html/colourSchemes/helix.html" />\r
+ <mapID target="colours.strand" url="html/colourSchemes/strand.html" />\r
+ <mapID target="colours.turn" url="html/colourSchemes/turn.html" />\r
+ <mapID target="colours.buried" url="html/colourSchemes/buried.html" />\r
+ <mapID target="colours.nucleotide" url="html/colourSchemes/nucleotide.html" />\r
+ <mapID target="colours.blosum" url="html/colourSchemes/blosum.html" />\r
+ <mapID target="colours.pid" url="html/colourSchemes/pid.html" />\r
+ <mapID target="colours.user" url="html/colourSchemes/user.html"/>\r
+ <mapID target="colours.abovepid" url="html/colourSchemes/abovePID.html"/>\r
+ <mapID target="colours.conservation" url="html/colourSchemes/conservation.html"/>\r
\r
<mapID target="aminoAcids" url="html/misc/aminoAcids.html" />\r
<mapID target="geneticCode" url="html/misc/geneticCode.html" />\r
<?xml version="1.0" encoding="ISO-8859-1" ?>\r
<!DOCTYPE index PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp Index Version 1.0//EN" "http://java.sun.com/products/javahelp/index_1_0.dtd">\r
<index version="1.0">\r
- <indexitem text="Menus">\r
- <indexitem text="File" target="home"/>\r
- <indexitem text="Edit" target="home"/>\r
- <indexitem text="Font" target="home"/>\r
- <indexitem text="View" target="home"/>\r
- <indexitem text="Colour" target="home"/>\r
- <indexitem text="Calculate" target="home"/>\r
- <indexitem text="Align" target="home"/>\r
+ <indexitem text="Jalview Documentation">\r
+ <indexitem text="Getting started" target="start"/>\r
+ <indexitem text="Whats new" target="new"/>\r
+ <indexitem text="Web Services" target="webservice"/>\r
+ <indexitem text="Input / Output" target="io"/>\r
+ <indexitem text="Editing Alignment" target="edit"/>\r
+ <indexitem text="Colour Schemes" target="colours"/>\r
+ <indexitem text="Calculating trees" target="trees"/>\r
+ <indexitem text="Conservation" target="conservation"/>\r
+ <indexitem text="Principal Component Analysis" target="pca"/>\r
</indexitem>\r
+ <indexitem text="Useful Information" target="home"/>\r
</index>\r
<?xml version="1.0" encoding="ISO-8859-1" ?>\r
<!DOCTYPE toc PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp TOC Version 1.0//EN" "http://java.sun.com/products/javahelp/toc_1_0.dtd">\r
<toc version="1.0">\r
-<tocitem text="Menus" expand="true" >\r
- <tocitem text="File" target="home"/>\r
- <tocitem text="Edit" target="home"/>\r
- <tocitem text="Font" target="home"/>\r
- <tocitem text="View" target="home"/>\r
- <tocitem text="Colour" target="colours">\r
+<tocitem text="Jalview Documentation" target="home" expand="true" >\r
+ <tocitem text="Getting Started" target="start"/>\r
+ <tocitem text="Whats new" target="new" expand="false">\r
+ <tocitem text="Search" target="search"/>\r
+ <tocitem text="Wrap Alignment" target="wrap"/>\r
+ <tocitem text="Overview Window" target ="overview"/>\r
+ <tocitem text="Sequence Features" target ="seqfeatures"/>\r
+ </tocitem>\r
+ <tocitem text="Web Services" target="webservice" expand="false">\r
+ <tocitem text="Clustal Alignment" target="clustal"/>\r
+ </tocitem>\r
+ <tocitem text="Input /Output" target="io"/>\r
+ <tocitem text="Editing Alignment" target ="edit"/>\r
+ <tocitem text="Colour Schemes" target="colours" expand="false">\r
+ <tocitem text="ClustalX" target="colours.clustal"/>\r
<tocitem text="Zappo" target="colours.zappo"/>\r
<tocitem text="Taylor" target="colours.taylor"/>\r
<tocitem text="Hydrophobicity" target="colours.hydro"/>\r
<tocitem text="Buried index" target="colours.buried"/>\r
<tocitem text="Nucleotide colours" target="colours.nucleotide"/>\r
<tocitem text="Blosum62" target="colours.blosum"/>\r
- <tocitem text="PID" target="colours.pid"/> \r
+ <tocitem text="by Percentage Identity" target="colours.pid"/> \r
+ <tocitem text="User Defined" target="colours.user"/>\r
+ <tocitem text="Above Percentage Identity" target="colours.abovepid"/>\r
+ <tocitem text="By conservation" target="colours.conservation"/>\r
+ </tocitem>\r
+ <tocitem text="Calculations" expand="false">\r
+ <tocitem text="Calculating trees" target="trees"/>\r
+ <tocitem text="Conservation" target="conservation"/>\r
+ <tocitem text="Principal Component Analysis" target="pca"/>\r
+ <tocitem text="Pairwise Alignments" target="pairwise"/>\r
+ <tocitem text="Remove Redundancy" target="redundancy"/>\r
</tocitem>\r
- <tocitem text="Calculate" target="calculate"/>\r
- <tocitem text="Align" target="home"/>\r
</tocitem>\r
-<tocitem text="Useful information">\r
+<tocitem text="Useful information" expand="false">\r
<tocitem text="Amino Acid Table" target="aminoAcids"/>\r
<tocitem text="The Genetic Code" target="geneticCode"/>\r
</tocitem>\r
--- /dev/null
+<html>\r
+<body>\r
+<p>Conservation </p>\r
+</body>\r
+</html>\r
--- /dev/null
+<html>\r
+<body>\r
+Tree \r
+</body>\r
+</html>\r
--- /dev/null
+<html>\r
+\r
+<body>\r
+<p>pca </p>\r
+</body>\r
+</html>\r
--- /dev/null
+<html>\r
+<body>\r
+tree \r
+</body>\r
+</html>\r
--- /dev/null
+<html>\r
+\r
+<body>\r
+tree \r
+</body>\r
+</html>\r
--- /dev/null
+<html>\r
+<head>\r
+<style type="text/css">\r
+<!--\r
+td {\r
+ text-align: center;\r
+}\r
+-->\r
+</style>\r
+</head>\r
+\r
+<body>\r
+<p> <em>Colouring above a percentage identity threshold</em></p>\r
+<p> Selecting this option causes the colour scheme to be applied to only those \r
+ residues that occur in that column more than a certain percentage of the time. \r
+ For instance selecting the threshold to be 100 will only colour those columns \r
+ with 100 % identity. This threshold option can be applied to the Zappo, Taylor, \r
+ Hydrophobicity and User colour schemes. </p>\r
+</body>\r
+</html>\r
--- /dev/null
+<html>\r
+<head>\r
+<style type="text/css">\r
+<!--\r
+td {\r
+ text-align: center;\r
+}\r
+-->\r
+</style>\r
+</head>\r
+\r
+<body>\r
+\r
+<p><em>Blosum62</a></em> </p>\r
+<p>Gaps are coloured white. If a residue matchs the consensus sequence residue\r
+ at that position it is colored dark blue. If it does not match the consensus\r
+ residue but the 2 residues have a positive Blosum62 score, it is colored light\r
+ blue.</p>\r
+</body>\r
+</html>\r
--- /dev/null
+<html>\r
+<head>\r
+<style type="text/css">\r
+<!--\r
+td {\r
+ text-align: center;\r
+}\r
+-->\r
+</style>\r
+</head>\r
+\r
+<body>\r
+<p><em>Buried index</em></p>\r
+<div align="center">\r
+ <table width="400" border="1">\r
+ <tr>\r
+ <td bgcolor="#0000ff">C</td>\r
+ <td bgcolor="#0054ab">I</td>\r
+ <td bgcolor="#005fa0">V</td>\r
+ <td bgcolor="#007b84">L</td>\r
+ <td bgcolor="#008778">F</td>\r
+ </tr>\r
+ <tr>\r
+ <td bgcolor="#009768">M</td>\r
+ <td bgcolor="#009d62">G</td>\r
+ <td bgcolor="#00a35c">A</td>\r
+ <td bgcolor="#00a857">W</td>\r
+ <td bgcolor="#00b649">X</td>\r
+ </tr>\r
+ <tr>\r
+ <td bgcolor="#00d52a">S</td>\r
+ <td bgcolor="#00d52a">H</td>\r
+ <td bgcolor="#00db24">T</td>\r
+ <td bgcolor="#00e01f">P</td>\r
+ <td bgcolor="#00e619">Y</td>\r
+ </tr>\r
+ <tr>\r
+ <td bgcolor="#00eb14">N</td>\r
+ <td bgcolor="#00eb14">B</td>\r
+ <td bgcolor="#00eb14">D</td>\r
+ <td bgcolor="#00f10e">Q</td>\r
+ <td bgcolor="#00f10e">Z</td>\r
+ </tr>\r
+ <tr> </td>\r
+ <td bgcolor="#00f10e">E</td>\r
+ <td bgcolor="#00fc03">R</td>\r
+ <td bgcolor="#00ff00">K</td>\r
+ </tr>\r
+ </table>\r
+</div>\r
+</body>\r
+</html>\r
--- /dev/null
+<html>\r
+<head>\r
+<style type="text/css">\r
+<!--\r
+td {\r
+ text-align: center;\r
+}\r
+-->\r
+</style>\r
+</head>\r
+\r
+<body>\r
+<p><em>Clustal X</em></p>\r
+<div align="center">\r
+ <table width="400" border="1">\r
+ <tr>\r
+ <td bgcolor="#ff0000">N</td>\r
+ <td bgcolor="#ff0000">G</td>\r
+ <td bgcolor="#f60909">P</td>\r
+ <td bgcolor="#f30c0c">B</td>\r
+ <td bgcolor="#e81717">D</td>\r
+ </tr>\r
+ <tr>\r
+ <td bgcolor="#e11e1e">S</td>\r
+ <td bgcolor="#a85757">C</td>\r
+ <td bgcolor="#9d6262">Y</td>\r
+ <td bgcolor="#7e8181">K</td>\r
+ <td bgcolor="#7c8383">X</td>\r
+ </tr>\r
+ <tr>\r
+ <td bgcolor="#778888">Q</td>\r
+ <td bgcolor="#738c8c">W</td>\r
+ <td bgcolor="#738c8c">T</td>\r
+ <td bgcolor="#708f8f">R</td>\r
+ <td bgcolor="#708f8f">H</td>\r
+ </tr>\r
+ <tr>\r
+ <td bgcolor="#5ba4a4">Z</td>\r
+ <td bgcolor="#3fc0c0">E</td>\r
+ <td bgcolor="#2cd3d3">A</td>\r
+ <td bgcolor="#1ee1e1">F</td>\r
+ <td bgcolor="#1ee1e1">M</td>\r
+ </tr>\r
+ <tr> </td>\r
+ <td bgcolor="#1ce3e3">L</td>\r
+ <td bgcolor="#07f8f8">V</td>\r
+ <td bgcolor="#00ffff">I</td>\r
+ </tr>\r
+ </table>\r
+</div>\r
+</body>\r
+</html>\r
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">\r
<html>\r
<head>\r
-<title>Untitled Document</title>\r
-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">\r
<style type="text/css">\r
<!--\r
td {\r
<body>\r
<p><em><a name="zappo">Zappo Colour</a>s</em><br>\r
<br>\r
- The residues are coloured according to their physico-chemical properties as \r
+ The residues are coloured according to their physico-chemical properties as\r
follows: </p>\r
<div align="center">\r
<table width="400" border="1">\r
- <tr> \r
+ <tr>\r
<td > Aliphatic/hydrophobic</td>\r
<td bgcolor="#ffafaf">ILVAM </td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td>Aromatic</td>\r
<td bgcolor="#ffc800">FWY</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td>Positive</td>\r
<td bgcolor="#6464ff">KRH</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td> Negative</td>\r
<td bgcolor="#ff0000">DE</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td>Hydrophilic</td>\r
<td bgcolor="#00ff00">STNQ</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td>conformationally special</td>\r
<td bgcolor="#ff00ff">PG</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td>Cysteine</td>\r
<td bgcolor="#ffff00">C</td>\r
</tr>\r
</div>\r
<p align="center"></p>\r
<p><em><a name="taylor">Taylor</a></em></p>\r
-<p>These colours were invented by Willie Taylor and an entertaining description \r
+<p>These colours were invented by Willie Taylor and an entertaining description\r
of their birth can be found in Protein Engineering, Vol 10 , 743-746 (1997)</p>\r
<div align="center">\r
<table width="400" border="1">\r
- <tr> \r
+ <tr>\r
<td bgcolor="#ccff00">A</td>\r
<td bgcolor="#99ff00">V</td>\r
<td bgcolor="#66ff00">I</td>\r
<td bgcolor="#33ff00">L</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td bgcolor="#00ff00">M</td>\r
<td bgcolor="#00ff66">F</td>\r
<td bgcolor="#00ffcc">Y</td>\r
<td bgcolor="#00ccff">W</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td bgcolor="#0066ff">H</td>\r
<td bgcolor="#0000ff">R</td>\r
<td bgcolor="#6600ff">K</td>\r
<td bgcolor="#cc00ff">N</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td bgcolor="#ff00cc">Q</td>\r
<td bgcolor="#ff0066">E</td>\r
<td bgcolor="#ff0000">D</td>\r
<td bgcolor="#ff3300">S</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td bgcolor="#ff6600">T</td>\r
<td bgcolor="#ff9900">G</td>\r
<td bgcolor="#ffcc00">P</td>\r
</div>\r
<p align="center"> </p>\r
<p><em><a name="hydrophobic">Hydrophobicity</a></em></p>\r
-<p>According to the hydrophobicity table of Kyte, J., and Doolittle, R.F., J. \r
- Mol. Biol. 1157, 105-132, 1982. The most hydrophobic residues according to this \r
+<p>According to the hydrophobicity table of Kyte, J., and Doolittle, R.F., J.\r
+ Mol. Biol. 1157, 105-132, 1982. The most hydrophobic residues according to this\r
table are coloured red and the most hydrophilic ones are coloured blue.</p>\r
<div align="center">\r
<table width="400" border="1">\r
- <tr> \r
+ <tr>\r
<td bgcolor="#ff0000">I</td>\r
<td bgcolor="#f60009">V</td>\r
<td bgcolor="#ea0015">L</td>\r
<td bgcolor="#cb0034">F</td>\r
<td bgcolor="#c2003d">C</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td bgcolor="#b0004f">M</td>\r
<td bgcolor="#ad0052">A</td>\r
<td bgcolor="#6a0095">G</td>\r
<td bgcolor="#680097">X</td>\r
<td bgcolor="#61009e">T</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td bgcolor="#5e00a1">S</td>\r
<td bgcolor="#5b00a4">W</td>\r
<td bgcolor="#4f00b0">Y</td>\r
<td bgcolor="#4600b9">P</td>\r
<td bgcolor="#1500ea">H</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td bgcolor="#0c00f3">E</td>\r
<td bgcolor="#0c00f3">Z</td>\r
<td bgcolor="#0c00f3">Q</td>\r
<p><em><a name="helix">Helix Propensity</a></em></p>\r
<div align="center">\r
<table width="400" border="1">\r
- <tr> \r
+ <tr>\r
<td bgcolor="#ff00ff">E</td>\r
<td bgcolor="#ef10ef">M</td>\r
<td bgcolor="#e718e7">A</td>\r
<td bgcolor="#c936c9">Z</td>\r
<td bgcolor="#ae51ae">L</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td bgcolor="#a05fa0">K</td>\r
<td bgcolor="#986798">F</td>\r
<td bgcolor="#926d92">Q</td>\r
<td bgcolor="#8a758a">I</td>\r
<td bgcolor="#8a758a">W</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td bgcolor="#857a85">V</td>\r
<td bgcolor="#778877">D</td>\r
<td bgcolor="#758a75">X</td>\r
<td bgcolor="#758a75">H</td>\r
<td bgcolor="#6f906f">R</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td bgcolor="#49b649">B</td>\r
<td bgcolor="#47b847">T</td>\r
<td bgcolor="#36c936">S</td>\r
<p><em><a name="strand">Strand propensity</a></em></p>\r
<div align="center">\r
<table width="400" border="1">\r
- <tr> \r
+ <tr>\r
<td bgcolor="#ffff00">V</td>\r
<td bgcolor="#ecec13">I</td>\r
<td bgcolor="#d3d32c">Y</td>\r
<td bgcolor="#c2c23d">F</td>\r
<td bgcolor="#c0c03f">W</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td bgcolor="#b2b24d">L</td>\r
<td bgcolor="#9d9d62">T</td>\r
<td bgcolor="#9d9d62">C</td>\r
<td bgcolor="#8c8c73">Q</td>\r
<td bgcolor="#82827d">M</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td bgcolor="#797986">X</td>\r
<td bgcolor="#6b6b94">R</td>\r
<td bgcolor="#64649b">N</td>\r
<td bgcolor="#60609f">H</td>\r
<td bgcolor="#5858a7">A</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td bgcolor="#4949b6">S</td>\r
<td bgcolor="#4949b6">G</td>\r
<td bgcolor="#4747b8">Z</td>\r
<p><em><a name="turn">Turn propensity</a></em></p>\r
<div align="center">\r
<table width="400" border="1">\r
- <tr> \r
+ <tr>\r
<td bgcolor="#ff0000">N</td>\r
<td bgcolor="#ff0000">G</td>\r
<td bgcolor="#f60909">P</td>\r
<td bgcolor="#f30c0c">B</td>\r
<td bgcolor="#e81717">D</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td bgcolor="#e11e1e">S</td>\r
<td bgcolor="#a85757">C</td>\r
<td bgcolor="#9d6262">Y</td>\r
<td bgcolor="#7e8181">K</td>\r
<td bgcolor="#7c8383">X</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td bgcolor="#778888">Q</td>\r
<td bgcolor="#738c8c">W</td>\r
<td bgcolor="#738c8c">T</td>\r
<td bgcolor="#708f8f">R</td>\r
<td bgcolor="#708f8f">H</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td bgcolor="#5ba4a4">Z</td>\r
<td bgcolor="#3fc0c0">E</td>\r
<td bgcolor="#2cd3d3">A</td>\r
<p><em><a name="buried"></a>Buried index</a></em></p>\r
<div align="center">\r
<table width="400" border="1">\r
- <tr> \r
+ <tr>\r
<td bgcolor="#0000ff">C</td>\r
<td bgcolor="#0054ab">I</td>\r
<td bgcolor="#005fa0">V</td>\r
<td bgcolor="#007b84">L</td>\r
<td bgcolor="#008778">F</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td bgcolor="#009768">M</td>\r
<td bgcolor="#009d62">G</td>\r
<td bgcolor="#00a35c">A</td>\r
<td bgcolor="#00a857">W</td>\r
<td bgcolor="#00b649">X</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td bgcolor="#00d52a">S</td>\r
<td bgcolor="#00d52a">H</td>\r
<td bgcolor="#00db24">T</td>\r
<td bgcolor="#00e01f">P</td>\r
<td bgcolor="#00e619">Y</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td bgcolor="#00eb14">N</td>\r
<td bgcolor="#00eb14">B</td>\r
<td bgcolor="#00eb14">D</td>\r
<p><em></em><a name="nucleotide">Nucleotide Colours</a></em></p>\r
<div align="center">\r
<table width="200" border="1">\r
- <tr> \r
+ <tr>\r
<td bgcolor="#64F73F">A</td>\r
<td bgcolor="#FFB340">C</td>\r
<td bgcolor="#EB413C">G</td>\r
</div>\r
<p align="center"> </p>\r
<p><em><a name="blosum"></a>Blosum62</a></em></p>\r
-<p>Gaps are coloured white. If a residue matchs the consensus sequence residue \r
- at that position it is colored dark blue. If it does not match the consensus \r
- residue but the 2 residues have a positive Blosum62 score, it is colored light \r
+<p>Gaps are coloured white. If a residue matchs the consensus sequence residue\r
+ at that position it is colored dark blue. If it does not match the consensus\r
+ residue but the 2 residues have a positive Blosum62 score, it is colored light\r
blue.</p>\r
<p> </p>\r
<p><em><a name="pid">Colouring above a percentage identity threshold</a></em><br>\r
- Selecting this option causes the colour scheme to be applied to only those residues \r
- that occur in that column more than a certain percentage of the time. For instance \r
- selecting the threshold to be 100 will only colour those columns with 100 % \r
- identity. This threshold option can be applied to the Zappo, Taylor, Hydrophobicity \r
+ Selecting this option causes the colour scheme to be applied to only those residues\r
+ that occur in that column more than a certain percentage of the time. For instance\r
+ selecting the threshold to be 100 will only colour those columns with 100 %\r
+ identity. This threshold option can be applied to the Zappo, Taylor, Hydrophobicity\r
and User colour schemes. <br>\r
- This option depends on a consensus calculation having been performed. If no \r
- consensus exists (e.g. after a copy or a clustalw alignment) then no residues \r
+ This option depends on a consensus calculation having been performed. If no\r
+ consensus exists (e.g. after a copy or a clustalw alignment) then no residues\r
are coloured.</p>\r
<p><em>PID Colours</em><br>\r
This depends on the applet having performed a consensus calculation on the alignment.<br>\r
- The PID option colours the residues (boxes and/or text) according to the percentage \r
- of the residues in each column that agree with the consensus sequence. Only \r
+ The PID option colours the residues (boxes and/or text) according to the percentage\r
+ of the residues in each column that agree with the consensus sequence. Only\r
the residues that agree with the consensus residue for each column are coloured.<br>\r
</p>\r
<p> </p>\r
--- /dev/null
+<html>\r
+<body>\r
+<p><em>Conservation Colours</em></p>\r
+<p>This option is based on the AMAS method of multiple sequence alignment analysis \r
+ (Livingstone C.D. and Barton G.J. (1993), Protein Sequence Alignments: A Strategy \r
+ for the Hierarchical Analysis of Residue Conservation.CABIOS Vol. 9 No. 6 (745-756)). \r
+ <br>\r
+ Hierarchical analysis is based on each residue having certain physico-chemical \r
+ properties.</p>\r
+<p>The alignment can first be divided into groups. This is best done by first \r
+ creating an average distance tree (Calculate->Average distance tree). Selecting \r
+ a position on the tree will cluster the sequences into groups depending on the \r
+ position selected. Each group is coloured a different colour which is used for \r
+ both the ids in the tree and alignment windows and the sequences themselves. \r
+ If a PCA window is visible a visual comparison can be made between the clustering \r
+ based on the tree and the PCA. </p>\r
+<p>The grouping by tree may not be satisfactory and the user may want to edit \r
+ the groups to put any outliers together. </p>\r
+<p>When the conservation option is selected the existing colour scheme is modified \r
+ so that the most conserved columns in each group have the most intense colours \r
+ and the least conserved are the palest.</p>\r
+<p> </p>\r
+</body>\r
+</html>\r
--- /dev/null
+<html>\r
+<head>\r
+<style type="text/css">\r
+<!--\r
+td {\r
+ text-align: center;\r
+}\r
+-->\r
+</style>\r
+</head>\r
+\r
+<body>\r
+<p><em>Helix Propensity</em> </p>\r
+<div align="center">\r
+ <table width="400" border="1">\r
+ <tr>\r
+ <td bgcolor="#ff00ff">E</td>\r
+ <td bgcolor="#ef10ef">M</td>\r
+ <td bgcolor="#e718e7">A</td>\r
+ <td bgcolor="#c936c9">Z</td>\r
+ <td bgcolor="#ae51ae">L</td>\r
+ </tr>\r
+ <tr>\r
+ <td bgcolor="#a05fa0">K</td>\r
+ <td bgcolor="#986798">F</td>\r
+ <td bgcolor="#926d92">Q</td>\r
+ <td bgcolor="#8a758a">I</td>\r
+ <td bgcolor="#8a758a">W</td>\r
+ </tr>\r
+ <tr>\r
+ <td bgcolor="#857a85">V</td>\r
+ <td bgcolor="#778877">D</td>\r
+ <td bgcolor="#758a75">X</td>\r
+ <td bgcolor="#758a75">H</td>\r
+ <td bgcolor="#6f906f">R</td>\r
+ </tr>\r
+ <tr>\r
+ <td bgcolor="#49b649">B</td>\r
+ <td bgcolor="#47b847">T</td>\r
+ <td bgcolor="#36c936">S</td>\r
+ <td bgcolor="#23dc23">C</td>\r
+ <td bgcolor="#21de21">Y</td>\r
+ </tr>\r
+ <tr> </td>\r
+ <td bgcolor="#1be41b">N</td>\r
+ <td bgcolor="#00ff00">G</td>\r
+ <td bgcolor="#00ff00">P</td>\r
+ </tr>\r
+ </table>\r
+</div>\r
+</body>\r
+</html>\r
--- /dev/null
+<html>\r
+<head>\r
+<style type="text/css">\r
+<!--\r
+td {\r
+ text-align: center;\r
+}\r
+-->\r
+</style>\r
+</head>\r
+\r
+<body>\r
+<p><em>Hydrophobicity</em></p>\r
+<p>According to the hydrophobicity table of Kyte, J., and Doolittle, R.F., J.\r
+ Mol. Biol. 1157, 105-132, 1982. The most hydrophobic residues according to this\r
+ table are coloured red and the most hydrophilic ones are coloured blue.</p>\r
+<div align="center">\r
+ <table width="400" border="1">\r
+ <tr>\r
+ <td bgcolor="#ff0000">I</td>\r
+ <td bgcolor="#f60009">V</td>\r
+ <td bgcolor="#ea0015">L</td>\r
+ <td bgcolor="#cb0034">F</td>\r
+ <td bgcolor="#c2003d">C</td>\r
+ </tr>\r
+ <tr>\r
+ <td bgcolor="#b0004f">M</td>\r
+ <td bgcolor="#ad0052">A</td>\r
+ <td bgcolor="#6a0095">G</td>\r
+ <td bgcolor="#680097">X</td>\r
+ <td bgcolor="#61009e">T</td>\r
+ </tr>\r
+ <tr>\r
+ <td bgcolor="#5e00a1">S</td>\r
+ <td bgcolor="#5b00a4">W</td>\r
+ <td bgcolor="#4f00b0">Y</td>\r
+ <td bgcolor="#4600b9">P</td>\r
+ <td bgcolor="#1500ea">H</td>\r
+ </tr>\r
+ <tr>\r
+ <td bgcolor="#0c00f3">E</td>\r
+ <td bgcolor="#0c00f3">Z</td>\r
+ <td bgcolor="#0c00f3">Q</td>\r
+ <td bgcolor="#0c00f3">D</td>\r
+ <td bgcolor="#0c00f3">B</td>\r
+ </tr>\r
+ <tr> </td>\r
+ <td bgcolor="#0c00f3">N</td>\r
+ <td bgcolor="#0000ff">K</td>\r
+ <td bgcolor="#0000ff">R</td>\r
+ </tr>\r
+ </table>\r
+</div>\r
+</body>\r
+</html>\r
--- /dev/null
+<html>\r
+\r
+<body>\r
+<p><strong>Colour schemes</strong></p>\r
+<p>Jalview allows the user to set a background colour for the whole alignment\r
+ and also set the colour of defined groups within the alignment. </p>\r
+<p>To change the background colour, simply select the colour from the "Colour"\r
+ menu.</p>\r
+<p>To change the colour of a group, right click on any residue within a group\r
+ and use the popup menu to define the group colour. </p>\r
+<p>At the top of the "Colour" menu the tick box "Apply Background\r
+ Colour to all groups". This is automatically ticked as default and means\r
+ the chosen colour will be applied to all existing groups. If you wish to maintain\r
+ the colour scheme for defined groups, make sure you deselect this option before\r
+ changing the background colour.</p>\r
+<p> </p>\r
+<p> </p>\r
+<p> </p>\r
+<p> </p>\r
+</body>\r
+</html>\r
--- /dev/null
+<html>\r
+<head>\r
+<style type="text/css">\r
+<!--\r
+td {\r
+ text-align: center;\r
+}\r
+-->\r
+</style>\r
+</head>\r
+\r
+<body>\r
+<p><em>Nucleotide Colours</em></p>\r
+<div align="center">\r
+ <table width="200" border="1">\r
+ <tr>\r
+ <td bgcolor="#64F73F">A</td>\r
+ <td bgcolor="#FFB340">C</td>\r
+ <td bgcolor="#EB413C">G</td>\r
+ <td bgcolor="#3C88EE">T</td>\r
+ </tr>\r
+ </table>\r
+</div>\r
+</body>\r
+</html>\r
--- /dev/null
+<html>\r
+<head>\r
+<style type="text/css">\r
+<!--\r
+td {\r
+ text-align: center;\r
+}\r
+-->\r
+</style>\r
+</head>\r
+\r
+<body>\r
+<p><em>PID Colours</em><br>\r
+ <br>\r
+ The PID option colours the residues (boxes and/or text) according to the percentage\r
+ of the residues in each column that agree with the consensus sequence. Only\r
+ the residues that agree with the consensus residue for each column are coloured.</p>\r
+<table width="200" border="1">\r
+ <tr>\r
+ <td bgcolor="#6464FF">> 80 %</td>\r
+ </tr>\r
+ <tr>\r
+ <td bgcolor="#9999FF">> 60 %</td>\r
+ </tr>\r
+ <tr>\r
+ <td bgcolor="#CCCCFF">> 40%</td>\r
+ </tr>\r
+ <tr>\r
+ <td>< 40%</td>\r
+ </tr>\r
+</table>\r
+</body>\r
+</html>\r
--- /dev/null
+<html>\r
+<head>\r
+<style type="text/css">\r
+<!--\r
+td {\r
+ text-align: center;\r
+}\r
+-->\r
+</style>\r
+</head>\r
+\r
+<body>\r
+<p><em>Strand propensity</em></p>\r
+<div align="center">\r
+ <table width="400" border="1">\r
+ <tr>\r
+ <td bgcolor="#ffff00">V</td>\r
+ <td bgcolor="#ecec13">I</td>\r
+ <td bgcolor="#d3d32c">Y</td>\r
+ <td bgcolor="#c2c23d">F</td>\r
+ <td bgcolor="#c0c03f">W</td>\r
+ </tr>\r
+ <tr>\r
+ <td bgcolor="#b2b24d">L</td>\r
+ <td bgcolor="#9d9d62">T</td>\r
+ <td bgcolor="#9d9d62">C</td>\r
+ <td bgcolor="#8c8c73">Q</td>\r
+ <td bgcolor="#82827d">M</td>\r
+ </tr>\r
+ <tr>\r
+ <td bgcolor="#797986">X</td>\r
+ <td bgcolor="#6b6b94">R</td>\r
+ <td bgcolor="#64649b">N</td>\r
+ <td bgcolor="#60609f">H</td>\r
+ <td bgcolor="#5858a7">A</td>\r
+ </tr>\r
+ <tr>\r
+ <td bgcolor="#4949b6">S</td>\r
+ <td bgcolor="#4949b6">G</td>\r
+ <td bgcolor="#4747b8">Z</td>\r
+ <td bgcolor="#4747b8">K</td>\r
+ <td bgcolor="#4343bc">B</td>\r
+ </tr>\r
+ <tr> </td>\r
+ <td bgcolor="#2323dc">P</td>\r
+ <td bgcolor="#2121de">D</td>\r
+ <td bgcolor="#0000ff">E</td>\r
+ </tr>\r
+ </table>\r
+</div>\r
+</body>\r
+</html>\r
--- /dev/null
+<html>\r
+<head>\r
+<style type="text/css">\r
+<!--\r
+td {\r
+ text-align: center;\r
+}\r
+-->\r
+</style>\r
+</head>\r
+\r
+<body>\r
+<p><em><a name="taylor">Taylor</a></em></p>\r
+<p>These colours were invented by Willie Taylor and an entertaining description\r
+ of their birth can be found in Protein Engineering, Vol 10 , 743-746 (1997)</p>\r
+<div align="center">\r
+ <table width="400" border="1">\r
+ <tr>\r
+ <td bgcolor="#ccff00">A</td>\r
+ <td bgcolor="#99ff00">V</td>\r
+ <td bgcolor="#66ff00">I</td>\r
+ <td bgcolor="#33ff00">L</td>\r
+ </tr>\r
+ <tr>\r
+ <td bgcolor="#00ff00">M</td>\r
+ <td bgcolor="#00ff66">F</td>\r
+ <td bgcolor="#00ffcc">Y</td>\r
+ <td bgcolor="#00ccff">W</td>\r
+ </tr>\r
+ <tr>\r
+ <td bgcolor="#0066ff">H</td>\r
+ <td bgcolor="#0000ff">R</td>\r
+ <td bgcolor="#6600ff">K</td>\r
+ <td bgcolor="#cc00ff">N</td>\r
+ </tr>\r
+ <tr>\r
+ <td bgcolor="#ff00cc">Q</td>\r
+ <td bgcolor="#ff0066">E</td>\r
+ <td bgcolor="#ff0000">D</td>\r
+ <td bgcolor="#ff3300">S</td>\r
+ </tr>\r
+ <tr>\r
+ <td bgcolor="#ff6600">T</td>\r
+ <td bgcolor="#ff9900">G</td>\r
+ <td bgcolor="#ffcc00">P</td>\r
+ <td bgcolor="#ffff00">C</td>\r
+ </tr>\r
+ </table>\r
+</div>\r
+</body>\r
+</html>\r
--- /dev/null
+<html>\r
+<head>\r
+<style type="text/css">\r
+<!--\r
+td {\r
+ text-align: center;\r
+}\r
+-->\r
+</style>\r
+</head>\r
+\r
+<body>\r
+<p><em>Turn propensity</em></p>\r
+<div align="center">\r
+ <table width="400" border="1">\r
+ <tr>\r
+ <td bgcolor="#ff0000">N</td>\r
+ <td bgcolor="#ff0000">G</td>\r
+ <td bgcolor="#f60909">P</td>\r
+ <td bgcolor="#f30c0c">B</td>\r
+ <td bgcolor="#e81717">D</td>\r
+ </tr>\r
+ <tr>\r
+ <td bgcolor="#e11e1e">S</td>\r
+ <td bgcolor="#a85757">C</td>\r
+ <td bgcolor="#9d6262">Y</td>\r
+ <td bgcolor="#7e8181">K</td>\r
+ <td bgcolor="#7c8383">X</td>\r
+ </tr>\r
+ <tr>\r
+ <td bgcolor="#778888">Q</td>\r
+ <td bgcolor="#738c8c">W</td>\r
+ <td bgcolor="#738c8c">T</td>\r
+ <td bgcolor="#708f8f">R</td>\r
+ <td bgcolor="#708f8f">H</td>\r
+ </tr>\r
+ <tr>\r
+ <td bgcolor="#5ba4a4">Z</td>\r
+ <td bgcolor="#3fc0c0">E</td>\r
+ <td bgcolor="#2cd3d3">A</td>\r
+ <td bgcolor="#1ee1e1">F</td>\r
+ <td bgcolor="#1ee1e1">M</td>\r
+ </tr>\r
+ <tr> </td>\r
+ <td bgcolor="#1ce3e3">L</td>\r
+ <td bgcolor="#07f8f8">V</td>\r
+ <td bgcolor="#00ffff">I</td>\r
+ </tr>\r
+ </table>\r
+</div>\r
+</body>\r
+</html>\r
--- /dev/null
+<html>\r
+\r
+<body>\r
+<p><em>User Defined Colours</em></p>\r
+<p>Each of the residues may be assigned a new user defined colour. </p>\r
+<p>You may save this colour scheme and reuse it at a later time.</p>\r
+<p>The default user defined colour is the last user colour scheme which was defined.</p>\r
+<p> </p>\r
+<p> </p>\r
+</body>\r
+</html>\r
--- /dev/null
+<html>\r
+<head>\r
+<style type="text/css">\r
+<!--\r
+td {\r
+ text-align: center;\r
+}\r
+-->\r
+</style>\r
+</head>\r
+\r
+<body>\r
+<p><em>Zappo Colours</em><br>\r
+ <br>\r
+ The residues are coloured according to their physico-chemical properties as\r
+ follows: </p>\r
+<div align="center">\r
+ <table width="400" border="1">\r
+ <tr>\r
+ <td > Aliphatic/hydrophobic</td>\r
+ <td bgcolor="#ffafaf">ILVAM </td>\r
+ </tr>\r
+ <tr>\r
+ <td>Aromatic</td>\r
+ <td bgcolor="#ffc800">FWY</td>\r
+ </tr>\r
+ <tr>\r
+ <td>Positive</td>\r
+ <td bgcolor="#6464ff">KRH</td>\r
+ </tr>\r
+ <tr>\r
+ <td> Negative</td>\r
+ <td bgcolor="#ff0000">DE</td>\r
+ </tr>\r
+ <tr>\r
+ <td>Hydrophilic</td>\r
+ <td bgcolor="#00ff00">STNQ</td>\r
+ </tr>\r
+ <tr>\r
+ <td>conformationally special</td>\r
+ <td bgcolor="#ff00ff">PG</td>\r
+ </tr>\r
+ <tr>\r
+ <td>Cysteine</td>\r
+ <td bgcolor="#ffff00">C</td>\r
+ </tr>\r
+ </table>\r
+</div>\r
+</body>\r
+</html>\r
--- /dev/null
+<html>\r
+\r
+<body>\r
+<p><strong>Editing</strong></p>\r
+<p><em>Inserting / removing gaps</em> - hold down the "Shift" key. Click\r
+ a residue with the mouse and drag the residue to the right to insert gaps or\r
+ to the left to remove gaps.<br>\r
+ If the residue selected is within a defined group, hold down either "Alt"\r
+ or "Control" key and drag the residue left or right to edit all sequences\r
+ in the defined group at once. </p>\r
+<p><em>Copy/paste/cut/delete</em> - any sequences which are in the current selection\r
+ box (indicated in red) may be cut and / or copied to a new alignment or deleted.\r
+</p>\r
+<p><em>Undo / redo</em> - editing of sequences (insertion/removal of gaps, removal\r
+ of sequences, trimming sequences etc) may be undone or redone at any time using\r
+ the appropriate menu items from the edit menu. The undo history list only allows\r
+ a maximum of 10 actions.\r
+<p><em>Trimming alignment</em> - First select a column by clicking the scale indicator\r
+ (above the sequences) The alignment may then be trimmed to the left or right\r
+ of this column. If multiple columns are selected, the alignment is trimmed to\r
+ the right of the rightmost selected column (or to the left of the leftmost selected\r
+ column)</p>\r
+<p><em>Remove gapped columns</em> - Removes columns within the alignment which\r
+ contain only space characters ("-" or "." or " ")</p>\r
+<p><em>Removing gaps</em> - Removes all gaps from the alignment. Gaps are "-"\r
+ or "." or " ".</p>\r
+<p><em>Set gap character</em> - Switches the gap character between "."\r
+ and "-". If the "Render Gaps" option from the "View"\r
+ menu is unticked all gaps will appear as blank spaces.</p>\r
+<p> </p>\r
+</body>\r
+</html>\r
--- /dev/null
+<html>\r
+<body>\r
+\r
+<p>Select the overview window to get a navigable image of the whole alignment.\r
+</p>\r
+<p>The window indicates the current viewable region of the alignment, this area\r
+ may be adjusted by clicking and dragging with the mouse.</p>\r
+<p>Note: It may not be possible to view very large alignments with the overview\r
+ window due to lack of application memory. </p>\r
+<p><img src="../images/overview.gif" width="407" height="137"></p>\r
+</body>\r
+</html>\r
--- /dev/null
+<html>\r
+<head>\r
+<style type="text/css">\r
+<!--\r
+td {\r
+ text-align: center;\r
+}\r
+-->\r
+</style>\r
+</head>\r
+\r
+<body>\r
+<p><strong>Search</strong></p>\r
+<p>The search box can be displayed by pressing the keys Control and F or selecting\r
+ "Search"</p>\r
+Note:\r
+<ul>\r
+ <li>The search will be performed on the selected region. If no region is selected,\r
+ the search will operate on the full alignment.</li>\r
+ <li>To clear any selection, press the "Escape" key.</li>\r
+</ul>\r
+<p>Using the "Create new group" is a quick way to group and highlight\r
+ residues with the specified search pattern throughout the alignment.</p>\r
+<p>The search allows regular expression matching. </p>\r
+<p> </p>\r
+<table width="100%" border="1">\r
+ <tr>\r
+ <td>.</td>\r
+ <td>Any single character.</td>\r
+ </tr>\r
+ <tr>\r
+ <td>[]</td>\r
+ <td>Any one of the characters in the brackets</td>\r
+ </tr>\r
+ <tr>\r
+ <td>^</td>\r
+ <td>The start of a line (column 1). </td>\r
+ </tr>\r
+ <tr>\r
+ <td>$</td>\r
+ <td>The end of a line </td>\r
+ </tr>\r
+ <tr>\r
+ <td>*</td>\r
+ <td> Matches zero or more of the preceding characters or expressions. </td>\r
+ </tr>\r
+ <tr>\r
+ <td>?</td>\r
+ <td>Matches zero or one of the preceding characters or expressions. </td>\r
+ </tr>\r
+ <tr>\r
+ <td>+</td>\r
+ <td>Matches one or more of the preceding characters or expressions. </td>\r
+ </tr>\r
+ <tr>\r
+ <td>{count}</td>\r
+ <td> Matches the specified number of the preceding characters or expressions.\r
+ </td>\r
+ </tr>\r
+ <tr>\r
+ <td>{min,}</td>\r
+ <td> Matches at least the specified number of the preceding characters or\r
+ expressions.</td>\r
+ </tr>\r
+ <tr>\r
+ <td>{min,max} </td>\r
+ <td>Matches between min and max of the preceding characters or expressions.</td>\r
+ </tr>\r
+</table>\r
+</body>\r
+</html>\r
--- /dev/null
+<html>\r
+<body>\r
+<p><strong>Sequence Features</strong></p>\r
+<p>This displays Uniprot sequence features on the alignment if a 100% sequence\r
+ match is found. </p>\r
+<p>The first step in this process is to match the id (name) of each sequence with\r
+ Uniprot. If there is no match, a Blast search is performed to try to obtain\r
+ the Uniprot Id for each sequence. You will be notified of any 100% matches with\r
+ Uniprot, which you must manually assign to each sequence in your input alignment,\r
+ then save the file.</p>\r
+<p>\r
+ The input sequence will be matched with the returned Uniprot record, the start\r
+ and end residues can then be correctly assigned to each sequence. </p>\r
+<p>Sequence features which are 1 residue in length are coloured red. Features\r
+ which span a region are coloured blue. </p>\r
+<p>By moving the mouse pointer over a sequence feature on the alignment a small\r
+ label will appear with the description of that sequence feature.</p>\r
+<p>A local cache of retrieved uniprot entries is recorded on your local machine.\r
+</p>\r
+</body>\r
+</html>\r
--- /dev/null
+<html>\r
+\r
+</head>\r
+\r
+<body>\r
+<p><strong>Wrap alignment </strong></p>\r
+<p>Use this feature to wrap an alignment to the screen width. </p>\r
+<p>All output (HTML, Printing, JPG etc) will also be in this wrapped format.</p>\r
+<p>This is most useful when looking at alignments with less than 20 sequences. \r
+</p>\r
+<p>Note: No editing is possible when the alignment is in "Wrapped" mode, \r
+ but all other features such as searching, calculations and changing the background \r
+ colour are unaffected.</p>\r
+<table width="480" border="1">\r
+ <tr><td>\r
+\r
+<table border="0" cellpadding="0" cellspacing="0">\r
+ <tr> \r
+ <td colspan="6"> </td>\r
+ <td colspan="9">10<br>\r
+ |</td>\r
+ <td></td>\r
+ <td colspan="9">20<br>\r
+ |</td>\r
+ <td></td>\r
+ </tr>\r
+ <tr> \r
+ <td nowrap>ADHR_DROPS/7-107 </td>\r
+ <td bgcolor="#e6331a">K</td>\r
+ <td bgcolor="#1ab3b3">H</td>\r
+ <td bgcolor="#80b3e6">V</td>\r
+ <td bgcolor="#80b3e6">C</td>\r
+ <td bgcolor="#1ab3b3">Y</td>\r
+ <td bgcolor="#80b3e6">V</td>\r
+ <td bgcolor="#80b3e6">A</td>\r
+ <td>D</td>\r
+ <td bgcolor="#80b3e6">C</td>\r
+ <td bgcolor="#e6994d">G</td>\r
+ <td bgcolor="#e6994d">G</td>\r
+ <td bgcolor="#80b3e6">I</td>\r
+ <td>A</td>\r
+ <td bgcolor="#80b3e6">L</td>\r
+ <td>E</td>\r
+ <td bgcolor="#1acc1a">T</td>\r
+ <td bgcolor="#1acc1a">S</td>\r
+ <td bgcolor="#e6331a">K</td>\r
+ <td bgcolor="#80b3e6">V</td>\r
+ <td bgcolor="#80b3e6">L</td>\r
+ <td bgcolor="#80b3e6">M</td>\r
+ <td>T</td>\r
+ <td bgcolor="#e6331a">K</td>\r
+ <td>N</td>\r
+ <td bgcolor="#80b3e6">I</td>\r
+ <td bgcolor="#80b3e6">A</td>\r
+ </tr>\r
+ <tr> \r
+ <td nowrap>ADH_DROHE/5-105 </td>\r
+ <td>S</td>\r
+ <td>N</td>\r
+ <td bgcolor="#80b3e6">I</td>\r
+ <td bgcolor="#80b3e6">I</td>\r
+ <td bgcolor="#80b3e6">F</td>\r
+ <td bgcolor="#80b3e6">V</td>\r
+ <td bgcolor="#80b3e6">A</td>\r
+ <td bgcolor="#e6994d">G</td>\r
+ <td bgcolor="#80b3e6">L</td>\r
+ <td bgcolor="#e6994d">G</td>\r
+ <td bgcolor="#e6994d">G</td>\r
+ <td bgcolor="#80b3e6">I</td>\r
+ <td bgcolor="#e6994d">G</td>\r
+ <td bgcolor="#80b3e6">L</td>\r
+ <td bgcolor="#cc4dcc">D</td>\r
+ <td bgcolor="#1acc1a">T</td>\r
+ <td bgcolor="#1acc1a">S</td>\r
+ <td bgcolor="#e6331a">R</td>\r
+ <td>E</td>\r
+ <td bgcolor="#80b3e6">I</td>\r
+ <td bgcolor="#80b3e6">V</td>\r
+ <td>K</td>\r
+ <td>S</td>\r
+ <td bgcolor="#e6994d">G</td>\r
+ <td bgcolor="#cccc00">P</td>\r
+ <td>K</td>\r
+ </tr>\r
+ <tr> \r
+ <td nowrap>PGDH_HUMAN/6-106 </td>\r
+ <td bgcolor="#e6331a">K</td>\r
+ <td bgcolor="#80b3e6">V</td>\r
+ <td bgcolor="#80b3e6">A</td>\r
+ <td bgcolor="#80b3e6">L</td>\r
+ <td bgcolor="#80b3e6">V</td>\r
+ <td bgcolor="#1acc1a">T</td>\r
+ <td bgcolor="#e6994d">G</td>\r
+ <td>A</td>\r
+ <td bgcolor="#80b3e6">A</td>\r
+ <td>Q</td>\r
+ <td bgcolor="#e6994d">G</td>\r
+ <td bgcolor="#80b3e6">I</td>\r
+ <td bgcolor="#e6994d">G</td>\r
+ <td>R</td>\r
+ <td>A</td>\r
+ <td>F</td>\r
+ <td>A</td>\r
+ <td bgcolor="#cc4dcc">E</td>\r
+ <td bgcolor="#80b3e6">A</td>\r
+ <td bgcolor="#80b3e6">L</td>\r
+ <td bgcolor="#80b3e6">L</td>\r
+ <td>L</td>\r
+ <td bgcolor="#e6331a">K</td>\r
+ <td bgcolor="#e6994d">G</td>\r
+ <td>.</td>\r
+ <td bgcolor="#80b3e6">A</td>\r
+ </tr>\r
+ <tr>\r
+ <td height="5"></td>\r
+ </tr>\r
+ <tr> \r
+ <td colspan="6"> </td>\r
+ <td colspan="9">36<br>\r
+ |</td>\r
+ <td></td>\r
+ <td colspan="9">46<br>\r
+ |</td>\r
+ <td></td>\r
+ </tr>\r
+ <tr> \r
+ <td nowrap>ADHR_DROPS/7-107 </td>\r
+ <td bgcolor="#e6331a">K</td>\r
+ <td bgcolor="#80b3e6">L</td>\r
+ <td bgcolor="#80b3e6">A</td>\r
+ <td bgcolor="#80b3e6">I</td>\r
+ <td bgcolor="#80b3e6">L</td>\r
+ <td>Q</td>\r
+ <td>S</td>\r
+ <td bgcolor="#80b3e6">V</td>\r
+ <td>E</td>\r
+ <td bgcolor="#1acc1a">N</td>\r
+ <td bgcolor="#cccc00">P</td>\r
+ <td bgcolor="#cccc00">P</td>\r
+ <td>.</td>\r
+ <td>.</td>\r
+ <td>.</td>\r
+ <td>.</td>\r
+ <td>.</td>\r
+ <td>.</td>\r
+ <td>.</td>\r
+ <td>.</td>\r
+ <td>A</td>\r
+ <td bgcolor="#80b3e6">I</td>\r
+ <td bgcolor="#80b3e6">A</td>\r
+ <td bgcolor="#1acc1a">Q</td>\r
+ <td bgcolor="#80b3e6">L</td>\r
+ <td>Q</td>\r
+ </tr>\r
+ <tr> \r
+ <td nowrap>ADH_DROHE/5-105 </td>\r
+ <td>N</td>\r
+ <td bgcolor="#80b3e6">L</td>\r
+ <td bgcolor="#80b3e6">V</td>\r
+ <td bgcolor="#80b3e6">V</td>\r
+ <td bgcolor="#80b3e6">L</td>\r
+ <td bgcolor="#cc4dcc">D</td>\r
+ <td>R</td>\r
+ <td bgcolor="#80b3e6">I</td>\r
+ <td bgcolor="#cc4dcc">D</td>\r
+ <td bgcolor="#1acc1a">N</td>\r
+ <td bgcolor="#cccc00">P</td>\r
+ <td bgcolor="#80b3e6">A</td>\r
+ <td>A</td>\r
+ <td>.</td>\r
+ <td>.</td>\r
+ <td>.</td>\r
+ <td>.</td>\r
+ <td>.</td>\r
+ <td>.</td>\r
+ <td>.</td>\r
+ <td>.</td>\r
+ <td bgcolor="#80b3e6">I</td>\r
+ <td bgcolor="#80b3e6">A</td>\r
+ <td bgcolor="#cc4dcc">E</td>\r
+ <td bgcolor="#80b3e6">L</td>\r
+ <td>K</td>\r
+ </tr>\r
+ <tr> \r
+ <td nowrap>PGDH_HUMAN/6-106 </td>\r
+ <td bgcolor="#e6331a">K</td>\r
+ <td bgcolor="#80b3e6">V</td>\r
+ <td bgcolor="#80b3e6">A</td>\r
+ <td bgcolor="#80b3e6">L</td>\r
+ <td bgcolor="#80b3e6">V</td>\r
+ <td bgcolor="#cc4dcc">D</td>\r
+ <td>W</td>\r
+ <td>N</td>\r
+ <td>L</td>\r
+ <td>E</td>\r
+ <td bgcolor="#80b3e6">A</td>\r
+ <td bgcolor="#e6994d">G</td>\r
+ <td>.</td>\r
+ <td>.</td>\r
+ <td>.</td>\r
+ <td>.</td>\r
+ <td>.</td>\r
+ <td>.</td>\r
+ <td>.</td>\r
+ <td>V</td>\r
+ <td>Q</td>\r
+ <td bgcolor="#80b3e6">C</td>\r
+ <td>K</td>\r
+ <td>A</td>\r
+ <td bgcolor="#80b3e6">A</td>\r
+ <td>L</td>\r
+ </tr>\r
+ <tr>\r
+ <td height="5"></td>\r
+ </tr>\r
+ <tr> \r
+ <td colspan="6"> </td>\r
+ <td colspan="9">62<br>\r
+ |</td>\r
+ <td></td>\r
+ <td colspan="9">72<br>\r
+ |</td>\r
+ <td></td>\r
+ </tr>\r
+ <tr> \r
+ <td nowrap>ADHR_DROPS/7-107 </td>\r
+ <td>S</td>\r
+ <td bgcolor="#80b3e6">I</td>\r
+ <td>K</td>\r
+ <td bgcolor="#1ab3b3">H</td>\r
+ <td>S</td>\r
+ <td>.</td>\r
+ <td>.</td>\r
+ <td>.</td>\r
+ <td>.</td>\r
+ <td>T</td>\r
+ <td>Q</td>\r
+ <td bgcolor="#80b3e6">I</td>\r
+ <td bgcolor="#80b3e6">F</td>\r
+ <td bgcolor="#80b3e6">F</td>\r
+ <td bgcolor="#80b3e6">W</td>\r
+ <td>T</td>\r
+ <td bgcolor="#80b3e6">F</td>\r
+ <td bgcolor="#cc4dcc">D</td>\r
+ <td bgcolor="#80b3e6">V</td>\r
+ <td bgcolor="#1acc1a">T</td>\r
+ <td bgcolor="#80b3e6">M</td>\r
+ <td bgcolor="#80b3e6">A</td>\r
+ <td>R</td>\r
+ <td bgcolor="#cc4dcc">E</td>\r
+ <td bgcolor="#cc4dcc">E</td>\r
+ <td>M</td>\r
+ </tr>\r
+ <tr> \r
+ <td nowrap>ADH_DROHE/5-105 </td>\r
+ <td>A</td>\r
+ <td bgcolor="#80b3e6">L</td>\r
+ <td>N</td>\r
+ <td bgcolor="#cccc00">P</td>\r
+ <td>.</td>\r
+ <td>.</td>\r
+ <td>.</td>\r
+ <td>.</td>\r
+ <td>K</td>\r
+ <td>V</td>\r
+ <td>T</td>\r
+ <td bgcolor="#80b3e6">I</td>\r
+ <td bgcolor="#1acc1a">T</td>\r
+ <td bgcolor="#80b3e6">F</td>\r
+ <td bgcolor="#1ab3b3">Y</td>\r
+ <td bgcolor="#cccc00">P</td>\r
+ <td bgcolor="#1ab3b3">Y</td>\r
+ <td bgcolor="#cc4dcc">D</td>\r
+ <td bgcolor="#80b3e6">V</td>\r
+ <td bgcolor="#1acc1a">T</td>\r
+ <td bgcolor="#80b3e6">V</td>\r
+ <td bgcolor="#cccc00">P</td>\r
+ <td>L</td>\r
+ <td>A</td>\r
+ <td bgcolor="#cc4dcc">E</td>\r
+ <td>T</td>\r
+ </tr>\r
+ <tr> \r
+ <td nowrap>PGDH_HUMAN/6-106 </td>\r
+ <td>D</td>\r
+ <td>E</td>\r
+ <td>Q</td>\r
+ <td bgcolor="#80b3e6">F</td>\r
+ <td>E</td>\r
+ <td bgcolor="#cccc00">P</td>\r
+ <td>.</td>\r
+ <td>.</td>\r
+ <td>.</td>\r
+ <td>Q</td>\r
+ <td>K</td>\r
+ <td bgcolor="#1acc1a">T</td>\r
+ <td bgcolor="#80b3e6">L</td>\r
+ <td bgcolor="#80b3e6">F</td>\r
+ <td bgcolor="#80b3e6">I</td>\r
+ <td>Q</td>\r
+ <td bgcolor="#80b3e6">C</td>\r
+ <td bgcolor="#cc4dcc">D</td>\r
+ <td bgcolor="#80b3e6">V</td>\r
+ <td>A</td>\r
+ <td>D</td>\r
+ <td>Q</td>\r
+ <td>Q</td>\r
+ <td bgcolor="#1acc1a">Q</td>\r
+ <td>L</td>\r
+ <td>.</td>\r
+ </tr>\r
+ <tr>\r
+ <td height="5"></td>\r
+ </tr>\r
+\r
+\r
+ </table>\r
+</table>\r
+\r
+\r
+</body>\r
+</html>\r
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">\r
<html>\r
-<head>\r
-<title>Untitled Document</title>\r
-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">\r
-</head>\r
\r
<body>\r
-<h1 align="center"><br>\r
- <img src="images/align.gif" width="200" height="80" align="baseline"> Jalview \r
- Documentation </h1>\r
-<p align="center">Your guide to Jalview</p>\r
+<p><img src="images/align.gif" width="200" height="80"><font size="4"> <strong>Jalview\r
+ Documentation</strong></font></p>\r
+<p> </p>\r
+JalView (1999) is a fast Java multiple alignment editor and analysis tool. It\r
+features many of the functions of AMAS, for the analysis of sub-families and the\r
+prediction of functional sites, but is fully interactive.\r
+<p></p>\r
+<p> If you use JalView in your work, please cite the bioinformatics paper: </p>\r
+<p>Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), "The Jalview\r
+ Java Alignment Editor", Bioinformatics, 12, 426-7.</p>\r
</body>\r
</html>\r
--- /dev/null
+<html>\r
+<body>\r
+<p><strong>Input</strong></p>\r
+<p>Jalview can read alignment files in any of the following formats:</p>\r
+<p><em>Fasta , MSF, Clustal, BLC, PIR, MSP, PFAM </em></p>\r
+<p>Use the menu at the top of the main application window to read in files from\r
+</p>\r
+<ul>\r
+ <li> the local file system</li>\r
+ <li>a remote website</li>\r
+ <li>or by copying and pasting into the "Cut & Paste" text window</li>\r
+</ul>\r
+<p>If a file is of an unknown format or there is any other error reading the alignment\r
+ file you will be given an error message, the alignment will not be read in.\r
+</p>\r
+<p><strong>Output</strong> </p>\r
+<p>Each alignment, whether it is the original or an edited version may be saved\r
+ in the formats</p>\r
+<p><em>Fasta , MSF, Clustal, BLC, PIR, MSP, PFAM </em></p>\r
+<p>The alignment may also be saved as a HTML web page. </p>\r
+<p>You may save a jpg image of your alignment. </p>\r
+<p>The alignment can be printed from a local printer.</p>\r
+</body>\r
+</html>\r
+++ /dev/null
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">\r
-<html>\r
-<head>\r
-<title>Untitled Document</title>\r
-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">\r
-</head>\r
-\r
-<body>\r
-Calculate menu<br>\r
-Consensus sequence <br>\r
-Sorting sequence by pairwise identity to consensus <br>\r
-Sorting by tree order <br>\r
-Sorting by group order <br>\r
-Removing redundancy of sequences <br>\r
-Smith-Waterman pairwise alignment <br>\r
-Principal component analysis <br>\r
-UPGMA tree using percentage identity distances <br>\r
-Neighbour joining tree using percentage identity distances <br>\r
-Conservation <br>\r
-<br>\r
-Consensus sequence<br>\r
-Each residue in the consensus sequence is the most frequent residue in each column \r
-of the alignment excluding gap residues ' ','-' and '.' . You can't access the \r
-consensus sequence directly but it is used in the PID colour scheme. <br>\r
-When the editor first starts up the consensus sequence is automatically calculated \r
-using all the sequences in the alignment and the PID colour scheme is used as \r
-default. If the consensus option is selected again only the currently selected \r
-sequences are used to calculate it and all sequences in the alignment are coloured \r
-according to that consensus. <br>\r
-<p>Sorting sequences<br>\r
- Once a consensus calculation has been done selecting this option will sort the \r
- selected sequences by their percentage identity to the consensus sequence. The \r
- most similar sequence is put at the top. If no sequences are selected then redundancy \r
- is removed from the whole alignment. <br>\r
- Sorting by tree order<br>\r
- If a UPGMA tree or a neighbour joining tree has been displayed then the main \r
- alignment window displays the sequences in the same order as they appear in \r
- the tree. This makes for easier comparison of the tree and the alignment. <br>\r
- <br>\r
- Sorting by group order<br>\r
- If the sequences have been grouped either by hand or by selecting a point on \r
- the tree then this option will reorder the alignment so all sequences in the \r
- same group are together. The largest group is shown at the top of the alignment \r
- and the smallest at the bottom. <br>\r
- Removing redundancy<br>\r
- Selecting this option brings up a window asking you to select a threshold. If \r
- the percentage identity between two sequences exceeds this value one of the \r
- sequences (the shorter) is discarded. The redundancy calculation is done when \r
- the Apply button is pressed. For large numbers of sequences this can take a \r
- long time as all pairs have to be compared. <br>\r
- Pairwise alignment (Proteins only)<br>\r
- This calculation is performed on the selected sequences only. Java is not the \r
- fastest language in the world and aligning more than a handful of sequences \r
- will take a fair amount of time. <br>\r
- For each pair of sequences the best global alignment is found using BLOSUM62 \r
- as the scoring matrix. The scores reported are the raw scores. The sequences \r
- are aligned using a dynamic programming technique and using the following gap \r
- penalties : </p>\r
-<p>Gap open : 12 <br>\r
- Gap extend : 2 </p>\r
-<p>When you select the pairwise alignment option a new window will come up which \r
- will display the alignments in a text format as they are calculated. Also displayed \r
- is information about the alignment such as alignment score, length and percentage \r
- identity between the sequences. </p>\r
-<p>If you want to save that pairwise alignment (it's not in any known format I'm \r
- afraid) you can cut and paste it from the text window with the mouse. You can \r
- also press the 'View in alignment editor' button to bring up another editor \r
- window. <br>\r
-</p>\r
-<p>Principal Component Analysis<br>\r
- This is a method of clustering sequences based on the method developed by G. \r
- Casari, C. Sander and A. Valencia. Structural Biology volume 2, no. 2, February \r
- 1995 . Extra information can also be found at the SeqSpace server at the EBI. \r
- <br>\r
- The version implemented here only looks at the clustering of whole sequences \r
- and not individual positions in the alignment to help identify functional residues. \r
- For large alignments plans are afoot to use the CORBA server written by Chris \r
- Dodge to do this 'residue space' PCA remotely. </p>\r
-<p>When the Calculate->Principal component analysis option is selected all \r
- the sequences (not just the selected ones) are used in the calculation and for \r
- large numbers of sequences this could take quite a time. When the calculation \r
- is finished a new window is displayed showing the projections of the sequences \r
- along the 2nd, 3rd and 4th vectors giving a 3dimensional view of how the sequences \r
- cluster. </p>\r
-<p>This 3d view can be rotated by holding the left mouse button down in the PCA \r
- window and moving it. The user can also zoom in and out by using the up and \r
- down arrow keys. </p>\r
-<p>Individual points can be selected using the mouse and selected sequences show \r
- up green in the PCA window and the usual grey background/white text in the alignment \r
- and tree windows. </p>\r
-<p>Different eigenvectors can be used to do the projection by changing the selected \r
- dimensions in the 3 menus underneath the 3d window. <br>\r
-</p>\r
-<p>UPGMA tree<br>\r
- If this option is selected from the Calculate menu then all sequences are used \r
- to generate a UPGMA tree. The pairwise distances used to cluster the sequences \r
- are the percentage mismatch between two sequences. For a reliable phylogenetic \r
- tree I recommend other programs (phylowin, phylip) should be used as they have \r
- the speed to use better distance methods and bootstrapping. Again, plans are \r
- afoot for a server to do this and to be able to read in tree files generated \r
- by other programs. <br>\r
- When the tree has been calculated a new window is displayed showing the tree \r
- with labels on the leaves showing the sequence ids. The user can select the \r
- ids with the mouse and the selected sequences will also be selected in the alignment \r
- window and the PCA window if that analysis has been calculated. </p>\r
-<p>Selecting the 'show distances' checkbox will put branch lengths on the branches. \r
- These branch lengths are the percentage mismatch between two nodes. </p>\r
-<p>Postscript output can be generated for this tree and mailed to you by clicking \r
- the Output button. This will bring up a window asking you for your email address \r
- and you can set font options and the page orientation. Clicking the Apply button \r
- will generate the postscript and send the email. <br>\r
-</p>\r
-<p>Neighbour Joining tree<br>\r
- The distances between sequences for this tree are generated in the same way \r
- as for the UPGMA tree. The method of clustering is the neighbour joining method \r
- which doesn't just pick the two closest leaves to cluster together but compensates \r
- for long edges by subtracting from the distances the average distance from each \r
- leaf to all the others. <br>\r
- Selection and output options are the same as for the UPGMA tree.</p>\r
-<p> Conservation<br>\r
- This option is based on the AMAS method of multiple sequence alignment analysis \r
- (Livingstone C.D. and Barton G.J. (1993), Protein Sequence Alignments: A Strategy \r
- for the Hierarchical Analysis of Residue Conservation.CABIOS Vol. 9 No. 6 (745-756)). \r
- <br>\r
- Hierarchical analysis is based on each residue having certain physico-chemical \r
- properties listed as follows: <br>\r
- <br>\r
- <br>\r
- <br>\r
-</p>\r
-<p>In brief go about it like this : <br>\r
-</p>\r
-<p>The alignment can first be divided into groups. This is best done by first \r
- creating an average distance tree (Calculate->Average distance tree). Selecting \r
- a position on the tree will cluster the sequences into groups depending on the \r
- position selected. Each group is coloured a different colour which is used for \r
- both the ids in the tree and alignment windows and the sequences themselves. \r
- If a PCA window is visible a visual comparison can be made between the clustering \r
- based on the tree and the PCA. <br>\r
- This link provides an example of the output after grouping for Pfam family rnaseH: \r
-</p>\r
-<p>The grouping by tree may not be satisfactory and the user may want to edit \r
- the groups (Edit->Groups...) to put any outliers together. </p>\r
-<p>Before selecting the conservation option change the colour scheme to something \r
- sensible (Taylor or hydrophobicity for example). When the conservation is done \r
- the existing colour scheme is modified so that the most conserved columns in \r
- each group have the most intense colours and the least conserved are the palest. \r
-</p>\r
-<p> </p>\r
-<p>This link shows the results of first colouring the alignment by hydrophobicity \r
- (Colour->by hydrophobicity) then performing conservation analysis (Calculate->Conservation). \r
- Conserved hydrophobic columns are shown with predominately red residues and \r
- conserved hydrophilic columns with blue. The most conserved regions have the \r
- brightest colours. <br>\r
-</p>\r
-<p> <br>\r
- <br>\r
- Here is shown the same conservation but with Taylor colours instead of hydrophobicity \r
- (Colour->Taylor). <br>\r
-</p>\r
-<p>The conservation analysis is done on each sequence group. This highlights differences \r
- and similarities in conserved residue properties between groups. </p>\r
-<p></p>\r
-</body>\r
-</html>\r
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">\r
<html>\r
<head>\r
-<title>Untitled Document</title>\r
-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">\r
<style type="text/css">\r
<!--\r
td {\r
<h2><br>\r
</h2>\r
<table WIDTH="441" BORDER ="5" cellpadding="3" BGCOLOR="#FFFFFF">\r
- <tr> \r
+ <tr>\r
<td width="15">A</td>\r
<td width="25">Ala</td>\r
<td width="157">Alanine</td>\r
<td width="192">GCT, GCC, GCA, GCG</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td>B</td>\r
<td> </td>\r
<td>either aspartic acid or asparagine</td>\r
<td> </td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td>C</td>\r
<td>Cys</td>\r
<td>Cysteine</td>\r
<td>TGT, TGC</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td>D</td>\r
<td>Asp</td>\r
<td>Aspartic Acid</td>\r
<td>GAT, GAC</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td>E</td>\r
<td>Glu</td>\r
<td>Glutamic Acid</td>\r
<td>GAA, GAG</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td>F</td>\r
<td>Phe</td>\r
<td>Phenylalanine</td>\r
<td>TTT, TTC</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td>G</td>\r
<td>Gly</td>\r
<td>Glycine</td>\r
<td>GGT, GGC, GGA, GGG</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td>H</td>\r
<td>His</td>\r
<td>Histidine</td>\r
<td>CAT, CAC</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td>I</td>\r
<td>Ile</td>\r
<td>Isoleucine</td>\r
<td>ATT, ATC, ATA</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td>K</td>\r
<td>Lys</td>\r
<td>Lysine</td>\r
<td>AAA, AAG</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td>L</td>\r
<td>Leu</td>\r
<td>Leucine</td>\r
<td>TTG, TTA, CTT, CTC, CTA, CTG</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td>M</td>\r
<td>Met</td>\r
<td>Methionine</td>\r
<td>ATG</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td>N</td>\r
<td>Asn</td>\r
<td>Asparagine</td>\r
<td>AAT, AAC</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td>P</td>\r
<td>Pro</td>\r
<td>Proline</td>\r
<td>CCT, CCC, CCA, CCG</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td>Q</td>\r
<td>Gln</td>\r
<td>Glutamine</td>\r
<td>CAA, CAG</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td>R</td>\r
<td>Arg</td>\r
<td>Arginine</td>\r
<td>CGT, CGC, CGA, CGG, AGA, AGG</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td>S</td>\r
<td>Ser</td>\r
<td>Serine</td>\r
<td>TCT, TCC, TCA, TCG, AGT, AGC</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td>T</td>\r
<td>Thr</td>\r
<td>Threonine</td>\r
<td>ACT, ACC, ACA, ACG</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td>V</td>\r
<td>Val</td>\r
<td>Valine</td>\r
<td>GTT, GTC, GTA, GTG</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td>W</td>\r
<td>Trp</td>\r
<td>Tryptophan</td>\r
<td>TGG</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td>X</td>\r
<td> </td>\r
<td>UNKNOWN</td>\r
<td> </td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td>Y</td>\r
<td>Tyr</td>\r
<td>Tyrosine</td>\r
<td>TAT, TAC</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td>Z</td>\r
<td> </td>\r
<td>either glutamic acid or glutamine</td>\r
<td> </td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td> </td>\r
<td>End</td>\r
<td>Terminator</td>\r
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">\r
<html>\r
<head>\r
-<title>Untitled Document</title>\r
-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">\r
<style type="text/css">\r
<!--\r
td {\r
<body>\r
\r
\r
-<div align="center"> \r
+<div align="center">\r
<h2>The Genetic Code </h2>\r
<table width="474" border="0">\r
- <tr> \r
+ <tr>\r
<td width="16%"> </td>\r
<td width="70%">2nd Position</td>\r
<td width="14%"> </td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td><p>1st Position</p>\r
<p>(5' end)</p></td>\r
<td><table border=5 cellpadding=3>\r
- <tr align=center bgcolor="#FFFFEE"> \r
+ <tr align=center bgcolor="#FFFFEE">\r
<td width="24"></td>\r
<td width="55"><h2>U</h2></td>\r
<td width="70"><h2>C</h2></td>\r
<td width="55"><h2>G</h2></td>\r
<td width="22"></td>\r
</tr>\r
- <tr align=center bgcolor="#FFFFEE"> \r
+ <tr align=center bgcolor="#FFFFEE">\r
<td><h1>U</h1></td>\r
<td>Phe<br>Phe<br>Leu<br>Leu</td>\r
<td>Ser<br>Ser<br>Ser<br>Ser</td>\r
<td>Tyr<br>Tyr<br>STOP</i><br>STOP</i></td>\r
<td>Cys<br>Cys<br>STOP</i><br>Trp</td>\r
- \r
+\r
<td>U<br>C<br>A<br>G</td>\r
</tr>\r
- <tr bgcolor="#FFFFEE"> \r
+ <tr bgcolor="#FFFFEE">\r
<td><h1>C</h1></td>\r
<td>Leu<br>Leu<br>Leu<br>Leu</td>\r
<td>Pro<br>Pro<br>Pro<br>Pro</td>\r
<td>Arg<br>Arg<br>Arg<br>Arg</td>\r
<td>U<br>C<br>A<br>G</td>\r
</tr>\r
- <tr bgcolor="#FFFFEE"> \r
+ <tr bgcolor="#FFFFEE">\r
<td><h1>A</h1></td>\r
<td>Ile<br>Ile<br>Ile<br>Met</td>\r
<td>Thr<br>Thr<br>Thr<br>Thr</td>\r
<td>Ser<br>Ser<br>Arg<br>Arg</td>\r
<td>U<br>C<br>A<br>G</td>\r
</tr>\r
- <tr bgcolor="#FFFFEE"> \r
+ <tr bgcolor="#FFFFEE">\r
<td><h1>G</h1></td>\r
<td>Val<br>Val<br>Val<br>Val</td>\r
<td>Ala<br>Ala<br>Ala<br>Ala</td>\r
--- /dev/null
+<html>\r
+\r
+<body>\r
+<p><strong>Getting started </strong></p>\r
+<p>Load a new </p>\r
+</body>\r
+</html>\r
--- /dev/null
+<html>\r
+<body>\r
+<p>Clustal alignment </p>\r
+</body>\r
+</html>\r
--- /dev/null
+<html>\r
+\r
+<body>\r
+Web service \r
+</body>\r
+</html>\r
--- /dev/null
+<html>\r
+\r
+<body>\r
+<p><strong>Whats new</strong> </p>\r
+<p>If you can read this then you'll already have seen some of the recent changes\r
+ made to Jalview.<br>\r
+</p>\r
+</body>\r
+</html>\r
--- /dev/null
+<html>\r
+<head>\r
+<title>Untitled Document</title>\r
+</head>\r
+\r
+<body>\r
+<p><img src="../images/align.gif" width="200" height="80"><font size="4"> \r
+ <strong>Jalview Documentation</strong></font></p>\r
+Whats new \r
+</body>\r
+</html>\r
git://source.jalview.org / jalview.git / commitdiff
