Conservation Calculation

From: amwaterhouse Date: Tue, 22 Feb 2005 12:20:21 +0000 (+0000) Subject: add titles X-Git-Tag: Release_2_0~640 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=3396e9f33cf3a16a7f38f5163cd057df4b859e7e;p=jalview.git add titles --- diff --git a/help/html/calculations/conservation.html b/help/html/calculations/conservation.html index 421e40f..24ba193 100755 --- a/help/html/calculations/conservation.html +++ b/help/html/calculations/conservation.html @@ -1,24 +1,25 @@ +Conservation Calculation

Conservation Calculation

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)). +

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 + 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 +

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 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 +

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 +

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

diff --git a/help/html/calculations/pairwise.html b/help/html/calculations/pairwise.html index a076b11..36c00b1 100755 --- a/help/html/calculations/pairwise.html +++ b/help/html/calculations/pairwise.html @@ -1,18 +1,19 @@ +Pairwise Alignment

Pairwise alignment (Proteins only)

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 +

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 + 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 :

Gap open : 12
Gap extend : 2

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 +

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.

diff --git a/help/html/calculations/pca.html b/help/html/calculations/pca.html index b48dae6..12fbab8 100755 --- a/help/html/calculations/pca.html +++ b/help/html/calculations/pca.html @@ -1,28 +1,28 @@ - +Principal Component Analysis

Principal Component Analysis

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. +

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 + 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. +

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 +

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 +

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 +

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

diff --git a/help/html/calculations/redundancy.html b/help/html/calculations/redundancy.html index 686b1df..1f3d464 100755 --- a/help/html/calculations/redundancy.html +++ b/help/html/calculations/redundancy.html @@ -1,10 +1,11 @@ +Removing Redundancy

Removing redundancy

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 +

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.

diff --git a/help/html/calculations/tree.html b/help/html/calculations/tree.html index e9a0908..16d7bbc 100755 --- a/help/html/calculations/tree.html +++ b/help/html/calculations/tree.html @@ -1,26 +1,26 @@ - +Tree Calculation

UPGMA tree

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. +

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 + 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. +

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

Neighbour Joining tree

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 +

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.

diff --git a/help/html/colourSchemes/abovePID.html b/help/html/colourSchemes/abovePID.html index 5f10c75..65e0e19 100755 --- a/help/html/colourSchemes/abovePID.html +++ b/help/html/colourSchemes/abovePID.html @@ -1,5 +1,5 @@ - +Above PID Colours - - - -

Zappo Colours
-
- The residues are coloured according to their physico-chemical properties as - follows:

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Aliphatic/hydrophobic	ILVAM
Aromatic	FWY
Positive	KRH
Negative	DE
Hydrophilic	STNQ
conformationally special	PG
Cysteine	C

Taylor

These colours were invented by Willie Taylor and an entertaining description - of their birth can be found in Protein Engineering, Vol 10 , 743-746 (1997)

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

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

Hydrophobicity

According to the hydrophobicity table of Kyte, J., and Doolittle, R.F., J. - Mol. Biol. 1157, 105-132, 1982. The most hydrophobic residues according to this - table are coloured red and the most hydrophilic ones are coloured blue.

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

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

Helix Propensity

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

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

Strand propensity

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

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

Turn propensity

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

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

Buried index

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

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

Nucleotide Colours

- - - - - - - -

Blosum62

Gaps are coloured white. If a residue matchs the consensus sequence residue - at that position it is colored dark blue. If it does not match the consensus - residue but the 2 residues have a positive Blosum62 score, it is colored light - blue.

Colouring above a percentage identity threshold
- Selecting this option causes the colour scheme to be applied to only those residues - that occur in that column more than a certain percentage of the time. For instance - selecting the threshold to be 100 will only colour those columns with 100 % - identity. This threshold option can be applied to the Zappo, Taylor, Hydrophobicity - and User colour schemes.
- This option depends on a consensus calculation having been performed. If no - consensus exists (e.g. after a copy or a clustalw alignment) then no residues - are coloured.

PID Colours
- This depends on the applet having performed a consensus calculation on the alignment.
- The PID option colours the residues (boxes and/or text) according to the percentage - of the residues in each column that agree with the consensus sequence. Only - the residues that agree with the consensus residue for each column are coloured.
-

- - diff --git a/help/html/colourSchemes/conservation.html b/help/html/colourSchemes/conservation.html index 6e8be7d..29756ba 100755 --- a/help/html/colourSchemes/conservation.html +++ b/help/html/colourSchemes/conservation.html @@ -1,23 +1,24 @@ +Conservation Calculation

Conservation Colours

The grouping by tree may not be satisfactory and the user may want to edit +

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

When the conservation option is selected the existing colour scheme is modified - so that the most conserved columns in each group have the most intense colours +

When the conservation option is selected 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.

diff --git a/help/html/colourSchemes/helix.html b/help/html/colourSchemes/helix.html index b59f1b6..f264c55 100755 --- a/help/html/colourSchemes/helix.html +++ b/help/html/colourSchemes/helix.html @@ -1,5 +1,5 @@ - +Helix Colour Scheme