<html>\r
+<head><title>Conservation Calculation</title></head>\r
<body>\r
<p><strong>Conservation Calculation</strong></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
+<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
+ 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
+<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
+<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>The existing colour scheme is modified so that the most conserved columns in \r
+<p>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</p>\r
-<p>The conservation analysis is done on each sequence group. This highlights differences \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
+<head><title>Pairwise Alignment</title></head>\r
<body>\r
<p><strong>Pairwise alignment (Proteins only)</strong></p>\r
-<p>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
+<p>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
+ 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
+<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> </p>\r
</body>\r
<html>\r
-\r
+<head><title>Principal Component Analysis</title></head>\r
<body>\r
<p><strong>Principal Component Analysis</strong></p>\r
-<p>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
+<p>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 implement a web service to do this 'residue \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 implement a web service to do this 'residue\r
space' PCA remotely. </p>\r
-<p>When the Principal component analysis option is selected all the sequences \r
- ( or just the selected ones) are used in the calculation and for large numbers \r
- of sequences this could take quite a time. When the calculation is finished \r
- a new window is displayed showing the projections of the sequences along the \r
- 2nd, 3rd and 4th vectors giving a 3dimensional view of how the sequences cluster. \r
+<p>When the Principal component analysis option is selected all the sequences\r
+ ( or just the selected ones) are used in the calculation and for large numbers\r
+ of sequences this could take quite a time. When the calculation is finished\r
+ a new window is displayed showing the projections of the sequences along the\r
+ 2nd, 3rd and 4th vectors giving a 3dimensional view of how the sequences cluster.\r
</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
+<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
+<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
+<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
</body>\r
<html>\r
+<head><title>Removing Redundancy</title></head>\r
<body>\r
<p><strong>Removing redundancy</strong></p>\r
-<p>Selecting this option brings up a window asking you to select a threshold. \r
- If 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
+<p>Selecting this option brings up a window asking you to select a threshold.\r
+ If 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. </p>\r
</body>\r
</html>\r
<html>\r
-\r
+<head><title>Tree Calculation</title></head>\r
<body>\r
<p><strong>UPGMA tree</strong></p>\r
-<p>If this option is selected then all sequences are used to generate a UPGMA \r
- tree. The pairwise distances used to cluster the sequences are the percentage \r
- mismatch between two sequences. For a reliable phylogenetic tree I recommend \r
- other programs (phylowin, phylip) should be used as they have the speed to use \r
- better distance methods and bootstrapping. Again, plans are afoot for a server \r
- to do this and to be able to read in tree files generated by other programs. \r
+<p>If this option is selected then all sequences are used to generate a UPGMA\r
+ tree. The pairwise distances used to cluster the sequences are the percentage\r
+ mismatch between two sequences. For a reliable phylogenetic tree I recommend\r
+ other programs (phylowin, phylip) should be used as they have the speed to use\r
+ better distance methods and bootstrapping. Again, plans are afoot for a server\r
+ to do this and to be able to read in tree files generated by other programs.\r
<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
+ 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
+<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> </p>\r
<p><strong>Neighbour Joining tree</strong></p>\r
-<p> 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
+<p> 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.<br>\r
</p>\r
<html>\r
-<head>\r
+<head><title>Above PID Colours</title>\r
<style type="text/css">\r
<!--\r
td {\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
+<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
<html>\r
-<head>\r
+<head><title>Blosum Colour Scheme</title>\r
<style type="text/css">\r
<!--\r
td {\r
<html>\r
-<head>\r
+<head><title>Buried Colour Scheme</title>\r
<style type="text/css">\r
<!--\r
td {\r
<html>\r
-<head>\r
+<head><title>Clustal Colour Scheme</title>\r
<style type="text/css">\r
<!--\r
td {\r
\r
<body>\r
<p><em>Clustal X</em></p>\r
-<div align="center"> \r
- <p>Clustal X is a graphical interface for the ClustalW multiple sequence alignment \r
- program. Sequences can be colored either by assigning a color to specific \r
- residues, or on the basis of an alignment consensus. The residues in each \r
- column are colored according to the consensus character assigned to that column. \r
- In this way, you can choose to highlight, for example, conserved hydrophylic \r
+<div align="center">\r
+ <p>Clustal X is a graphical interface for the ClustalW multiple sequence alignment\r
+ program. Sequences can be colored either by assigning a color to specific\r
+ residues, or on the basis of an alignment consensus. The residues in each\r
+ column are colored according to the consensus character assigned to that column.\r
+ In this way, you can choose to highlight, for example, conserved hydrophylic\r
or hydrophobic positions in the alignment. </p>\r
<p></p>\r
</div>\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="zappo">Zappo Colour</a>s</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
-<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
- 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
-<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
- 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
-<p align="center"> </p>\r
-<p><em><a name="helix">Helix Propensity</a></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
-<p align="center"> </p>\r
-<p><em><a name="strand">Strand propensity</a></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
-<p align="center"> </p>\r
-<p><em><a name="turn">Turn propensity</a></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
-<p align="center"> </p>\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
- <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
-<p align="center"> </p>\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
- <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
-<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
- 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
- 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
- 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 residues that agree with the consensus residue for each column are coloured.<br>\r
-</p>\r
-<p> </p>\r
-<p> </p>\r
-</body>\r
-</html>\r
<html>\r
+<head><title>Conservation Calculation</title></head>\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
+<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
+ 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
+<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
+<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
+<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
-<head>\r
+<head><title>Helix Colour Scheme</title>\r
<style type="text/css">\r
<!--\r
td {\r
<html>\r
-<head>\r
+<head><title>Hydrophobic Colour Scheme</title>\r
<style type="text/css">\r
<!--\r
td {\r
<html>\r
-\r
+<head><title>Colour Schemes</title></head>\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
<html>\r
-<head>\r
+<head><title>Nucleotide Colour Scheme</title>\r
<style type="text/css">\r
<!--\r
td {\r
<html>\r
-<head>\r
+<head><title>Percentage Identity Colour Scheme</title>\r
<style type="text/css">\r
<!--\r
td {\r
<html>\r
-<head>\r
+<head><title>Strand Colour Scheme</title>\r
<style type="text/css">\r
<!--\r
td {\r
<html>\r
-<head>\r
+<head><title>Taylor Colour Scheme</title>\r
<style type="text/css">\r
<!--\r
td {\r
<html>\r
-<head>\r
+<head><title>Turn Colour Scheme</title>\r
<style type="text/css">\r
<!--\r
td {\r
<html>\r
-\r
+<head><title>User Defined Colours</title></head>\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
<html>\r
-<head>\r
+<head><title>Zappo Colour Scheme</title>\r
<style type="text/css">\r
<!--\r
td {\r
<html>\r
-\r
+<head><title>Editing</title></head>\r
<body>\r
<p><strong>Editing</strong></p>\r
<p><em>Inserting / removing gaps</em> - hold down the "Shift" key. Click\r
<html>\r
+<head><title>Overview</title></head>\r
<body>\r
\r
<p>Select the overview window to get a navigable image of the whole alignment.\r
<html>\r
-<head>\r
+<head><title>Search</title>\r
<style type="text/css">\r
<!--\r
td {\r
<html>\r
+<head><title>Sequence Features</title></head>\r
<body>\r
<p><strong>Sequence Features</strong></p>\r
<p>This displays Uniprot sequence features on the alignment if a 100% sequence\r
<html>\r
\r
-</head>\r
+<head><title>Wrap Alignment</title></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>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
+<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
+ <tr>\r
<td colspan="6"> </td>\r
<td colspan="9">10<br>\r
|</td>\r
|</td>\r
<td></td>\r
</tr>\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">I</td>\r
<td bgcolor="#80b3e6">A</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td nowrap>ADH_DROHE/5-105 </td>\r
<td>S</td>\r
<td>N</td>\r
<td bgcolor="#cccc00">P</td>\r
<td>K</td>\r
</tr>\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
<tr>\r
<td height="5"></td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td colspan="6"> </td>\r
<td colspan="9">36<br>\r
|</td>\r
|</td>\r
<td></td>\r
</tr>\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">L</td>\r
<td>Q</td>\r
</tr>\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">L</td>\r
<td>K</td>\r
</tr>\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
<tr>\r
<td height="5"></td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td colspan="6"> </td>\r
<td colspan="9">62<br>\r
|</td>\r
|</td>\r
<td></td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td nowrap>ADHR_DROPS/7-107 </td>\r
<td>S</td>\r
<td bgcolor="#80b3e6">I</td>\r
<td bgcolor="#cc4dcc">E</td>\r
<td>M</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td nowrap>ADH_DROHE/5-105 </td>\r
<td>A</td>\r
<td bgcolor="#80b3e6">L</td>\r
<td bgcolor="#cc4dcc">E</td>\r
<td>T</td>\r
</tr>\r
- <tr> \r
+ <tr>\r
<td nowrap>PGDH_HUMAN/6-106 </td>\r
<td>D</td>\r
<td>E</td>\r
<html>\r
+<head><title>Home Page</title></head>\r
\r
<body>\r
<p><img src="images/align.gif" width="200" height="80"><font size="4"> <strong>Jalview\r
<html>\r
+<head><title>Input/Ouput</title></head>\r
<body>\r
<p><strong>Input</strong></p>\r
<p>Jalview can read alignment files in any of the following formats:</p>\r
<html>\r
-<head>\r
+<head><title>Amino Acids</title>\r
<style type="text/css">\r
<!--\r
td {\r
<html>\r
-<head>\r
+<head><title>Genetic Code</title>\r
<style type="text/css">\r
<!--\r
td {\r
<html>\r
+<head><title>Clustal Alignment</title></head>\r
<body>\r
<p><strong>Clustal Alignment</strong></p>\r
-<p> When this option is selected a progress window will appear giving you a message \r
- about whether your process is running. The alignment is sent to the Barton Group \r
+<p> When this option is selected a progress window will appear giving you a message\r
+ about whether your process is running. The alignment is sent to the Barton Group\r
cluster and remotely aligned using Clustalw program.</p>\r
-<p>When the alignment is finished a new alignment window is created with the aligned \r
+<p>When the alignment is finished a new alignment window is created with the aligned\r
sequences in.</p>\r
<p> </p>\r
</body>\r
<html>\r
-\r
+<head><title>Web Services</title></head>\r
<body>\r
<p><strong>Web services </strong></p>\r
-<p>Originally Jalview used SRS server to retrieve sequence features for a given \r
- alignment. In addition certain remote alignment programs could be called from \r
+<p>Originally Jalview used SRS server to retrieve sequence features for a given\r
+ alignment. In addition certain remote alignment programs could be called from\r
the Jalview interface and the results displayed in a new alignment panel. </p>\r
-<p>The main emphasis of the current development of the Jalview Project is to implement \r
- various sequence alignment programs, tree analysis, PCA algorithms on a large \r
- cluster based witihin the Barton Group. Jalview will be able to call these remote \r
+<p>The main emphasis of the current development of the Jalview Project is to implement\r
+ various sequence alignment programs, tree analysis, PCA algorithms on a large\r
+ cluster based witihin the Barton Group. Jalview will be able to call these remote\r
procedures without the user having to install any new software. <br>\r
- The main advantage of using these remote web services is that the computing \r
+ The main advantage of using these remote web services is that the computing\r
power available is much greater than that of the users work station.</p>\r
</body>\r
</html>\r
<html>\r
-\r
+<head><title>Whats new</title></head>\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
+<p>If you can read this then you'll already have seen some of the recent changes\r
made to Jalview.<br>\r
- Jalview takes advantage of some of the more recent user interface developments \r
- in the Java programming language. For instance Jalview is now a multi windowed \r
- application, this keeps all your Jalview windows neatly together in one main \r
+ Jalview takes advantage of some of the more recent user interface developments\r
+ in the Java programming language. For instance Jalview is now a multi windowed\r
+ application, this keeps all your Jalview windows neatly together in one main\r
application window. </p>\r
-<p>If you were familiar with the original Jalview, here is a list of important \r
+<p>If you were familiar with the original Jalview, here is a list of important\r
features you should know about the current development:</p>\r
<ul>\r
- <li>Editing sequences is no longer the default when mouse clicking the alignment. \r
- Instead, mouse clicking on the alignment will create a "selection region" \r
+ <li>Editing sequences is no longer the default when mouse clicking the alignment.\r
+ Instead, mouse clicking on the alignment will create a "selection region"\r
which may be full sequences or groups of residues.</li>\r
<li>To edit a sequence, the "Shift" key must be held down</li>\r
- <li>To edit groups, either the "Alt" key or the "Control" \r
+ <li>To edit groups, either the "Alt" key or the "Control"\r
key must be held down.</li>\r
- <li>Colours maybe applied to the background, ie the whole alignment, or to selected \r
- regions. If the tickbox "Apply colour to all groups" is ticked (this \r
+ <li>Colours maybe applied to the background, ie the whole alignment, or to selected\r
+ regions. If the tickbox "Apply colour to all groups" is ticked (this\r
is the defualt), then the colour will be applied to all groups.</li>\r
- <li>Use the right mouse button (apple and click on the mac) to define a selected \r
+ <li>Use the right mouse button (apple and click on the mac) to define a selected\r
region on the alignment as a new group. </li>\r
<li>Conservation is automatically updated whenever the alignment is edited</li>\r
<li>There is no "quick draw" option</li>\r
git://source.jalview.org / jalview.git / commitdiff