This option is based on the AMAS method of multiple sequence alignment analysis + (Livingstone C.D. and Barton G.J. (1993), Protein Sequence Alignments: A Strategy + for the Hierarchical Analysis of Residue Conservation.CABIOS Vol. 9 No. 6 (745-756)). +
+ Hierarchical analysis is based on each residue having certain physico-chemical + properties.

The alignment can first be divided into groups. This is best done by first + creating an average distance tree (Calculate->Average distance tree). Selecting + a position on the tree will cluster the sequences into groups depending on the + position selected. Each group is coloured a different colour which is used for + both the ids in the tree and alignment windows and the sequences themselves. + If a PCA window is visible a visual comparison can be made between the clustering + based on the tree and the PCA.

The grouping by tree may not be satisfactory and the user may want to edit + the groups to put any outliers together.

The existing colour scheme is modified so that the most conserved columns in + each group have the most intense colours and the least conserved are the palest

The conservation analysis is done on each sequence group. This highlights differences + and similarities in conserved residue properties between groups.

This calculation is performed on the selected sequences only. Java is not the + fastest language in the world and aligning more than a handful of sequences + will take a fair amount of time.
+ For each pair of sequences the best global alignment is found using BLOSUM62 + as the scoring matrix. The scores reported are the raw scores. The sequences + are aligned using a dynamic programming technique and using the following gap + penalties :

When you select the pairwise alignment option a new window will come up which + will display the alignments in a text format as they are calculated. Also displayed + is information about the alignment such as alignment score, length and percentage + identity between the sequences.

This is a method of clustering sequences based on the method developed by G. + Casari, C. Sander and A. Valencia. Structural Biology volume 2, no. 2, February + 1995 . Extra information can also be found at the SeqSpace server at the EBI. +
+ The version implemented here only looks at the clustering of whole sequences + and not individual positions in the alignment to help identify functional residues. + For large alignments plans are afoot to implement a web service to do this 'residue + space' PCA remotely.

When the Principal component analysis option is selected all the sequences + ( or just the selected ones) are used in the calculation and for large numbers + of sequences this could take quite a time. When the calculation is finished + a new window is displayed showing the projections of the sequences along the + 2nd, 3rd and 4th vectors giving a 3dimensional view of how the sequences cluster. +

This 3d view can be rotated by holding the left mouse button down in the PCA + window and moving it. The user can also zoom in and out by using the up and + down arrow keys.

Individual points can be selected using the mouse and selected sequences show + up green in the PCA window and the usual grey background/white text in the alignment + and tree windows.

Different eigenvectors can be used to do the projection by changing the selected + dimensions in the 3 menus underneath the 3d window.
+

Selecting this option brings up a window asking you to select a threshold. + If the percentage identity between two sequences exceeds this value one of the + sequences (the shorter) is discarded. The redundancy calculation is done when + the Apply button is pressed. For large numbers of sequences this can take a + long time as all pairs have to be compared.

If this option is selected then all sequences are used to generate a UPGMA + tree. The pairwise distances used to cluster the sequences are the percentage + mismatch between two sequences. For a reliable phylogenetic tree I recommend + other programs (phylowin, phylip) should be used as they have the speed to use + better distance methods and bootstrapping. Again, plans are afoot for a server + to do this and to be able to read in tree files generated by other programs. +
+ When the tree has been calculated a new window is displayed showing the tree + with labels on the leaves showing the sequence ids. The user can select the + ids with the mouse and the selected sequences will also be selected in the alignment + window and the PCA window if that analysis has been calculated.

Selecting the 'show distances' checkbox will put branch lengths on the branches. + These branch lengths are the percentage mismatch between two nodes.

The distances between sequences for this tree are generated in the same way + as for the UPGMA tree. The method of clustering is the neighbour joining method + which doesn't just pick the two closest leaves to cluster together but compensates + for long edges by subtracting from the distances the average distance from each + leaf to all the others.
+ Selection and output options are the same as for the UPGMA tree.
+

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N	G	P	B	D
S	C	Y	K	X
Q	W	T	R	H
Z	E	A	F	M
L	V	I

Clustal X is a graphical interface for the ClustalW multiple sequence alignment + program. Sequences can be colored either by assigning a color to specific + residues, or on the basis of an alignment consensus. The residues in each + column are colored according to the consensus character assigned to that column. + In this way, you can choose to highlight, for example, conserved hydrophylic + or hydrophobic positions in the alignment.

diff --git a/help/html/features/search.html b/help/html/features/search.html index e983765..5318162 100755 --- a/help/html/features/search.html +++ b/help/html/features/search.html @@ -25,8 +25,8 @@ Note:

- - + + diff --git a/help/html/start.html b/help/html/start.html deleted file mode 100755 index f2cb343..0000000 --- a/help/html/start.html +++ /dev/null @@ -1,7 +0,0 @@ - - - -

Getting started

Load a new

- - diff --git a/help/html/webServices/clustal.html b/help/html/webServices/clustal.html index deedf6d..d4065cc 100755 --- a/help/html/webServices/clustal.html +++ b/help/html/webServices/clustal.html @@ -1,5 +1,11 @@ -

Clustal alignment

Clustal Alignment

When this option is selected a progress window will appear giving you a message + about whether your process is running. The alignment is sent to the Barton Group + cluster and remotely aligned using Clustalw program.

When the alignment is finished a new alignment window is created with the aligned + sequences in.

diff --git a/help/html/webServices/index.html b/help/html/webServices/index.html index df43c57..2b24bfe 100755 --- a/help/html/webServices/index.html +++ b/help/html/webServices/index.html @@ -1,6 +1,15 @@ -Web service +

Web services

Originally Jalview used SRS server to retrieve sequence features for a given + alignment. In addition certain remote alignment programs could be called from + the Jalview interface and the results displayed in a new alignment panel.

The main emphasis of the current development of the Jalview Project is to implement + various sequence alignment programs, tree analysis, PCA algorithms on a large + cluster based witihin the Barton Group. Jalview will be able to call these remote + procedures without the user having to install any new software.
+ The main advantage of using these remote web services is that the computing + power available is much greater than that of the users work station.

diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 3af69ae..ec40290 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -2,8 +2,29 @@

Whats new

If you can read this then you'll already have seen some of the recent changes +

If you can read this then you'll already have seen some of the recent changes made to Jalview.
-

+ Jalview takes advantage of some of the more recent user interface developments + in the Java programming language. For instance Jalview is now a multi windowed + application, this keeps all your Jalview windows neatly together in one main + application window.

If you were familiar with the original Jalview, here is a list of important + features you should know about the current development:

Editing sequences is no longer the default when mouse clicking the alignment. + Instead, mouse clicking on the alignment will create a "selection region" + which may be full sequences or groups of residues.
To edit a sequence, the "Shift" key must be held down
To edit groups, either the "Alt" key or the "Control" + key must be held down.
Colours maybe applied to the background, ie the whole alignment, or to selected + regions. If the tickbox "Apply colour to all groups" is ticked (this + is the defualt), then the colour will be applied to all groups.
Use the right mouse button (apple and click on the mac) to define a selected + region on the alignment as a new group.
Conservation is automatically updated whenever the alignment is edited
There is no "quick draw" option
Edits can be undone! (and redone)

-- 1.7.10.2

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