From: amwaterhouse Date: Mon, 21 Feb 2005 16:59:02 +0000 (+0000) Subject: Updated help pages X-Git-Tag: Release_2_0~648 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=6fa9683bef52d6709abb81840681e4fa452cafe7;p=jalview.git Updated help pages --- diff --git a/help/help.jhm b/help/help.jhm index 363ee88..627a8c0 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -2,20 +2,41 @@ + - + + + + + - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/help/helpIndex.xml b/help/helpIndex.xml index 7d62840..d38cad8 100755 --- a/help/helpIndex.xml +++ b/help/helpIndex.xml @@ -1,13 +1,16 @@ - - - - - - - - + + + + + + + + + + + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index c49436d..38fe9da 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -1,12 +1,21 @@ - - - - - - + + + + + + + + + + + + + + + @@ -16,12 +25,20 @@ - + + + + + + + + + + + - - - + diff --git a/help/html/calculations/conservation.html b/help/html/calculations/conservation.html new file mode 100755 index 0000000..8c17f68 --- /dev/null +++ b/help/html/calculations/conservation.html @@ -0,0 +1,5 @@ + + +

Conservation

+ + diff --git a/help/html/calculations/pairwise.html b/help/html/calculations/pairwise.html new file mode 100755 index 0000000..4ad69ca --- /dev/null +++ b/help/html/calculations/pairwise.html @@ -0,0 +1,5 @@ + + +Tree + + diff --git a/help/html/calculations/pca.html b/help/html/calculations/pca.html new file mode 100755 index 0000000..5f67fc2 --- /dev/null +++ b/help/html/calculations/pca.html @@ -0,0 +1,6 @@ + + + +

pca

+ + diff --git a/help/html/calculations/redundancy.html b/help/html/calculations/redundancy.html new file mode 100755 index 0000000..0e07e65 --- /dev/null +++ b/help/html/calculations/redundancy.html @@ -0,0 +1,5 @@ + + +tree + + diff --git a/help/html/calculations/tree.html b/help/html/calculations/tree.html new file mode 100755 index 0000000..3d62766 --- /dev/null +++ b/help/html/calculations/tree.html @@ -0,0 +1,6 @@ + + + +tree + + diff --git a/help/html/colourSchemes/abovePID.html b/help/html/colourSchemes/abovePID.html new file mode 100755 index 0000000..5f10c75 --- /dev/null +++ b/help/html/colourSchemes/abovePID.html @@ -0,0 +1,20 @@ + + + + + + +

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.

+ + diff --git a/help/html/colourSchemes/blosum.html b/help/html/colourSchemes/blosum.html new file mode 100755 index 0000000..d08f977 --- /dev/null +++ b/help/html/colourSchemes/blosum.html @@ -0,0 +1,20 @@ + + + + + + + +

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.

+ + diff --git a/help/html/colourSchemes/buried.html b/help/html/colourSchemes/buried.html new file mode 100755 index 0000000..4e3933e --- /dev/null +++ b/help/html/colourSchemes/buried.html @@ -0,0 +1,52 @@ + + + + + + +

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

+ + diff --git a/help/html/colourSchemes/clustal.html b/help/html/colourSchemes/clustal.html new file mode 100755 index 0000000..488f745 --- /dev/null +++ b/help/html/colourSchemes/clustal.html @@ -0,0 +1,52 @@ + + + + + + +

Clustal X

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

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

+ + diff --git a/help/html/colourSchemes/colourSchemes.html b/help/html/colourSchemes/colourSchemes.html index 4264d38..69cef46 100755 --- a/help/html/colourSchemes/colourSchemes.html +++ b/help/html/colourSchemes/colourSchemes.html @@ -1,8 +1,5 @@ - -Untitled Document - + + + +

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

+ + diff --git a/help/html/colourSchemes/hydrophobic.html b/help/html/colourSchemes/hydrophobic.html new file mode 100755 index 0000000..d49e49b --- /dev/null +++ b/help/html/colourSchemes/hydrophobic.html @@ -0,0 +1,55 @@ + + + + + + +

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

+ + diff --git a/help/html/colourSchemes/index.html b/help/html/colourSchemes/index.html new file mode 100755 index 0000000..e5a9299 --- /dev/null +++ b/help/html/colourSchemes/index.html @@ -0,0 +1,21 @@ + + + +

Colour schemes

Jalview allows the user to set a background colour for the whole alignment + and also set the colour of defined groups within the alignment.

To change the background colour, simply select the colour from the "Colour" + menu.

To change the colour of a group, right click on any residue within a group + and use the popup menu to define the group colour.

At the top of the "Colour" menu the tick box "Apply Background + Colour to all groups". This is automatically ticked as default and means + the chosen colour will be applied to all existing groups. If you wish to maintain + the colour scheme for defined groups, make sure you deselect this option before + changing the background colour.

+ + diff --git a/help/html/colourSchemes/nucleotide.html b/help/html/colourSchemes/nucleotide.html new file mode 100755 index 0000000..5f4d47b --- /dev/null +++ b/help/html/colourSchemes/nucleotide.html @@ -0,0 +1,25 @@ + + + + + + +

Nucleotide Colours

+ + + + + + + +

+ + diff --git a/help/html/colourSchemes/pid.html b/help/html/colourSchemes/pid.html new file mode 100755 index 0000000..7eb3af7 --- /dev/null +++ b/help/html/colourSchemes/pid.html @@ -0,0 +1,33 @@ + + + + + + +

PID Colours
+
+ 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.

+ + + + + + + + + + + + + +

> 80 %

> 60 %

> 40%

< 40%

+ + diff --git a/help/html/colourSchemes/strand.html b/help/html/colourSchemes/strand.html new file mode 100755 index 0000000..7efe618 --- /dev/null +++ b/help/html/colourSchemes/strand.html @@ -0,0 +1,52 @@ + + + + + + +

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

+ + diff --git a/help/html/colourSchemes/taylor.html b/help/html/colourSchemes/taylor.html new file mode 100755 index 0000000..f7f0302 --- /dev/null +++ b/help/html/colourSchemes/taylor.html @@ -0,0 +1,51 @@ + + + + + + +

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

+ + diff --git a/help/html/colourSchemes/turn.html b/help/html/colourSchemes/turn.html new file mode 100755 index 0000000..b171e08 --- /dev/null +++ b/help/html/colourSchemes/turn.html @@ -0,0 +1,52 @@ + + + + + + +

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

+ + diff --git a/help/html/colourSchemes/user.html b/help/html/colourSchemes/user.html new file mode 100755 index 0000000..2021a64 --- /dev/null +++ b/help/html/colourSchemes/user.html @@ -0,0 +1,11 @@ + + + +

User Defined Colours

Each of the residues may be assigned a new user defined colour.

You may save this colour scheme and reuse it at a later time.

The default user defined colour is the last user colour scheme which was defined.

+ + diff --git a/help/html/colourSchemes/zappo.html b/help/html/colourSchemes/zappo.html new file mode 100755 index 0000000..95ac008 --- /dev/null +++ b/help/html/colourSchemes/zappo.html @@ -0,0 +1,50 @@ + + + + + + +

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

+ + diff --git a/help/html/editing/index.html b/help/html/editing/index.html new file mode 100755 index 0000000..89344fe --- /dev/null +++ b/help/html/editing/index.html @@ -0,0 +1,32 @@ + + + +

Editing

Inserting / removing gaps - hold down the "Shift" key. Click + a residue with the mouse and drag the residue to the right to insert gaps or + to the left to remove gaps.
+ If the residue selected is within a defined group, hold down either "Alt" + or "Control" key and drag the residue left or right to edit all sequences + in the defined group at once.

Copy/paste/cut/delete - any sequences which are in the current selection + box (indicated in red) may be cut and / or copied to a new alignment or deleted. +

Undo / redo - editing of sequences (insertion/removal of gaps, removal + of sequences, trimming sequences etc) may be undone or redone at any time using + the appropriate menu items from the edit menu. The undo history list only allows + a maximum of 10 actions. +

Trimming alignment - First select a column by clicking the scale indicator + (above the sequences) The alignment may then be trimmed to the left or right + of this column. If multiple columns are selected, the alignment is trimmed to + the right of the rightmost selected column (or to the left of the leftmost selected + column)

Remove gapped columns - Removes columns within the alignment which + contain only space characters ("-" or "." or " ")

Removing gaps - Removes all gaps from the alignment. Gaps are "-" + or "." or " ".

Set gap character - Switches the gap character between "." + and "-". If the "Render Gaps" option from the "View" + menu is unticked all gaps will appear as blank spaces.

+ + diff --git a/help/html/features/overview.html b/help/html/features/overview.html new file mode 100755 index 0000000..0a1d8b2 --- /dev/null +++ b/help/html/features/overview.html @@ -0,0 +1,12 @@ + + + +

Select the overview window to get a navigable image of the whole alignment. +

The window indicates the current viewable region of the alignment, this area + may be adjusted by clicking and dragging with the mouse.

Note: It may not be possible to view very large alignments with the overview + window due to lack of application memory.

+ + diff --git a/help/html/features/search.html b/help/html/features/search.html new file mode 100755 index 0000000..e983765 --- /dev/null +++ b/help/html/features/search.html @@ -0,0 +1,71 @@ + + + + + + +

Search

The search box can be displayed by pressing the keys Control and F or selecting + "Search"

+Note: +

The search will be performed on the selected region. If no region is selected, + the search will operate on the full alignment.
To clear any selection, press the "Escape" key.

Using the "Create new group" is a quick way to group and highlight + residues with the specified search pattern throughout the alignment.

The search allows regular expression matching.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

.	Any single character.
[]	Any one of the characters in the brackets
^	The start of a line (column 1).
$	The end of a line
*	Matches zero or more of the preceding characters or expressions.
?	Matches zero or one of the preceding characters or expressions.
+	Matches one or more of the preceding characters or expressions.
{count}	Matches the specified number of the preceding characters or expressions. +
{min,}	Matches at least the specified number of the preceding characters or + expressions.
{min,max}	Matches between min and max of the preceding characters or expressions.

+ + diff --git a/help/html/features/seqfeatures.html b/help/html/features/seqfeatures.html new file mode 100755 index 0000000..467818d --- /dev/null +++ b/help/html/features/seqfeatures.html @@ -0,0 +1,21 @@ + + +

Sequence Features

This displays Uniprot sequence features on the alignment if a 100% sequence + match is found.

The first step in this process is to match the id (name) of each sequence with + Uniprot. If there is no match, a Blast search is performed to try to obtain + the Uniprot Id for each sequence. You will be notified of any 100% matches with + Uniprot, which you must manually assign to each sequence in your input alignment, + then save the file.

+ The input sequence will be matched with the returned Uniprot record, the start + and end residues can then be correctly assigned to each sequence.

Sequence features which are 1 residue in length are coloured red. Features + which span a region are coloured blue.

By moving the mouse pointer over a sequence feature on the alignment a small + label will appear with the description of that sequence feature.

A local cache of retrieved uniprot entries is recorded on your local machine. +

+ + diff --git a/help/html/features/wrap.html b/help/html/features/wrap.html new file mode 100755 index 0000000..b02df8a --- /dev/null +++ b/help/html/features/wrap.html @@ -0,0 +1,322 @@ + + + + + +

Wrap alignment

Use this feature to wrap an alignment to the screen width.

All output (HTML, Printing, JPG etc) will also be in this wrapped format.

This is most useful when looking at alignments with less than 20 sequences. +

Note: No editing is possible when the alignment is in "Wrapped" mode, + but all other features such as searching, calculations and changing the background + colour are unaffected.

+ +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

10
+ |

20
+ |

ADHR_DROPS/7-107

ADH_DROHE/5-105

PGDH_HUMAN/6-106

36
+ |

46
+ |

ADHR_DROPS/7-107

ADH_DROHE/5-105

PGDH_HUMAN/6-106

62
+ |

72
+ |

ADHR_DROPS/7-107

ADH_DROHE/5-105

PGDH_HUMAN/6-106

+ + + + diff --git a/help/html/images/overview.gif b/help/html/images/overview.gif new file mode 100755 index 0000000..b5b1bc5 Binary files /dev/null and b/help/html/images/overview.gif differ diff --git a/help/html/index.html b/help/html/index.html index c9a98b0..460c5b9 100755 --- a/help/html/index.html +++ b/help/html/index.html @@ -1,14 +1,15 @@ - - -Untitled Document - - -

- Jalview - Documentation

Your guide to Jalview

Jalview + Documentation

+JalView (1999) is a fast Java multiple alignment editor and analysis tool. It +features many of the functions of AMAS, for the analysis of sub-families and the +prediction of functional sites, but is fully interactive. +

If you use JalView in your work, please cite the bioinformatics paper:

Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), "The Jalview + Java Alignment Editor", Bioinformatics, 12, 426-7.

diff --git a/help/html/io/index.html b/help/html/io/index.html new file mode 100755 index 0000000..73945ba --- /dev/null +++ b/help/html/io/index.html @@ -0,0 +1,24 @@ + + +

Input

Jalview can read alignment files in any of the following formats:

Fasta , MSF, Clustal, BLC, PIR, MSP, PFAM

Use the menu at the top of the main application window to read in files from +

the local file system
a remote website
or by copying and pasting into the "Cut & Paste" text window

If a file is of an unknown format or there is any other error reading the alignment + file you will be given an error message, the alignment will not be read in. +

Output

Each alignment, whether it is the original or an edited version may be saved + in the formats

Fasta , MSF, Clustal, BLC, PIR, MSP, PFAM

The alignment may also be saved as a HTML web page.

You may save a jpg image of your alignment.

The alignment can be printed from a local printer.

+ + diff --git a/help/html/menus/calculateMenu.html b/help/html/menus/calculateMenu.html deleted file mode 100755 index f73d63c..0000000 --- a/help/html/menus/calculateMenu.html +++ /dev/null @@ -1,165 +0,0 @@ - - - -Untitled Document - - - - -Calculate menu
-Consensus sequence
-Sorting sequence by pairwise identity to consensus
-Sorting by tree order
-Sorting by group order
-Removing redundancy of sequences
-Smith-Waterman pairwise alignment
-Principal component analysis
-UPGMA tree using percentage identity distances
-Neighbour joining tree using percentage identity distances
-Conservation
-
-Consensus sequence
-Each residue in the consensus sequence is the most frequent residue in each column -of the alignment excluding gap residues ' ','-' and '.' . You can't access the -consensus sequence directly but it is used in the PID colour scheme.
-When the editor first starts up the consensus sequence is automatically calculated -using all the sequences in the alignment and the PID colour scheme is used as -default. If the consensus option is selected again only the currently selected -sequences are used to calculate it and all sequences in the alignment are coloured -according to that consensus.
-

Sorting sequences
- Once a consensus calculation has been done selecting this option will sort the - selected sequences by their percentage identity to the consensus sequence. The - most similar sequence is put at the top. If no sequences are selected then redundancy - is removed from the whole alignment.
- Sorting by tree order
- If a UPGMA tree or a neighbour joining tree has been displayed then the main - alignment window displays the sequences in the same order as they appear in - the tree. This makes for easier comparison of the tree and the alignment.
-
- Sorting by group order
- If the sequences have been grouped either by hand or by selecting a point on - the tree then this option will reorder the alignment so all sequences in the - same group are together. The largest group is shown at the top of the alignment - and the smallest at the bottom.
- 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 - long time as all pairs have to be compared.
- 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 - 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 :

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 - identity between the sequences.

If you want to save that pairwise alignment (it's not in any known format I'm - afraid) you can cut and paste it from the text window with the mouse. You can - also press the 'View in alignment editor' button to bring up another editor - window.
-

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. -
- 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 use the CORBA server written by Chris - Dodge to do this 'residue space' PCA remotely.

When the Calculate->Principal component analysis option is selected all - the sequences (not 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.
-

UPGMA tree
- If this option is selected from the Calculate menu 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.

Postscript output can be generated for this tree and mailed to you by clicking - the Output button. This will bring up a window asking you for your email address - and you can set font options and the page orientation. Clicking the Apply button - will generate the postscript and send the email.
-

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 - leaf to all the others.
- Selection and output options are the same as for the UPGMA tree.

Conservation
- 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 listed as follows:
-
-
-
-

In brief go about it like this :
-

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.
- This link provides an example of the output after grouping for Pfam family rnaseH: -

The grouping by tree may not be satisfactory and the user may want to edit - the groups (Edit->Groups...) to put any outliers together.

Before selecting the conservation option change the colour scheme to something - sensible (Taylor or hydrophobicity for example). When the conservation is done - 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. -

This link shows the results of first colouring the alignment by hydrophobicity - (Colour->by hydrophobicity) then performing conservation analysis (Calculate->Conservation). - Conserved hydrophobic columns are shown with predominately red residues and - conserved hydrophilic columns with blue. The most conserved regions have the - brightest colours.
-

-
- Here is shown the same conservation but with Taylor colours instead of hydrophobicity - (Colour->Taylor).
-

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/misc/aminoAcids.html b/help/html/misc/aminoAcids.html index 3f19aac..45f38d3 100755 --- a/help/html/misc/aminoAcids.html +++ b/help/html/misc/aminoAcids.html @@ -1,8 +1,5 @@ - -Untitled Document -