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<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
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-<p>Conservation </p>\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
+ <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>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
+ and similarities in conserved residue properties between groups. </p>\r
+<p></p>\r
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-Tree \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
+ 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> </p>\r
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-<p>pca </p>\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
+ <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
+ 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>\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
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-tree \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
+ long time as all pairs have to be compared. </p>\r
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-tree \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
+ <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> </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
+ leaf to all the others. <br>\r
+ Selection and output options are the same as for the UPGMA tree.<br>\r
+</p>\r
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<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 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
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- <td>.</td>\r
- <td>Any single character.</td>\r
+ <td width="24%">.</td>\r
+ <td width="76%">Any single character.</td>\r
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<td>[]</td>\r
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-<p><strong>Getting started </strong></p>\r
-<p>Load a new </p>\r
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<body>\r
-<p>Clustal alignment </p>\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
+ 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
+ sequences in.</p>\r
+<p> </p>\r
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-Web service \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
+ 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
+ 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
+ power available is much greater than that of the users work station.</p>\r
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<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
-</p>\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
+ 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
+ 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
+ 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
+ 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
+ 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
+ <li>Edits can be undone! (and redone)</li>\r
+</ul>\r
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git://source.jalview.org / jalview.git / commitdiff