From: janengelhardt Date: Mon, 23 May 2011 17:54:19 +0000 (+0200) Subject: 'Help files updated with RNA stuff' merge; JAL-580 X-Git-Tag: Jalview_2_9~576^2~40 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=dfabc2facf04bc805f0b6001b94de3c62b3049b0;p=jalview.git 'Help files updated with RNA stuff' merge; JAL-580 Change-Id: Ib14678b4f39e99bb8816d744320f9072558ff38c --- diff --git a/help/help.jhm b/help/help.jhm index 0ed676c..0fd8d65 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -70,11 +70,15 @@ + + + + diff --git a/help/helpTOC.html b/help/helpTOC.html new file mode 100644 index 0000000..1a40c72 --- /dev/null +++ b/help/helpTOC.html @@ -0,0 +1,97 @@ +Jalview - Help + +

Contents

+ +
Jalview Documentation +
   What's new +
      Graduated Feature Colours +
      Sort by Features +
      Envision2 Service +
      Release History +
   Editing Alignments +
   Cursor Mode +
   Key Strokes +
   Input / Output +
   Making Figures +
   Hidden Regions +
   Multiple Views +
   Viewing Trees +
   Fetching Sequences +
   Sequence Features +
      Sequence Feature Settings +
      Sequence Features File +
      Feature Colourschemes +
      User Defined Sequence Features +
      Editing Sequence Features +
      DAS Feature Retrieval +
      DAS Feature Settings +
   Web Services +
      Sequence Alignment +
         Clustal Alignment +
         Muscle Alignment +
         MAFFT Alignment +
         Multiple Alignment Subjobs +
      Secondary Structure Prediction +
      Sequence Retrieval +
      Database Reference Retrieval +
      DAS Feature Retrieval +
   Nucleic Acid Support +
   Colour Schemes +
      Background Dependent Text Colour +
      ClustalX +
      Zappo +
      Taylor +
      Hydrophobicity +
      Helix propensity +
      Strand propensity +
      Turn propensity +
      Buried index +
      Nucleotide colours +
      Purine/Pyrimidine colours +
      Blosum62 +
      by Percentage Identity +
      User Defined +
      Above Percentage Identity +
      By conservation +
      By Annotation +
      By RNA Helices +
   Calculations +
      Sorting alignments +
      Calculating trees +
      Principal Component Analysis +
      Tree/PCA Input Data +
      Pairwise Alignments +
      Remove Redundancy +
   Alignment Annotations +
      Conservation +
      Quality +
      Consensus +
      Annotations File Format +
   Viewing PDB Files +
      Jmol Viewer +
      Simple PDB Viewer +
   VAMSAS Data Exchange +
   Window Menus +
      Desktop Window +
      Alignment Window +
         File Menu +
         Edit Menu +
         Select Menu +
         View Menu +
         Format Menu +
         Colour Menu +
         Calculation Menu +
         Web Service Menu +
         Annotation Menus +
         Popup Menu +
   Preferences +
   Memory Settings +
      JNLP with extra memory parameters +
   Command Line +
      Command Line Arguments +
      Groovy Shell +
   Privacy +
Useful information +
   Amino Acid Table +
   Amino Acid Properties +
   The Genetic Code diff --git a/help/helpTOC.xml b/help/helpTOC.xml index 3e41ba3..c7371d2 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -35,6 +35,7 @@ + @@ -70,12 +71,14 @@ + + diff --git a/help/html/colourSchemes/index.html b/help/html/colourSchemes/index.html index 79a6012..5af7721 100755 --- a/help/html/colourSchemes/index.html +++ b/help/html/colourSchemes/index.html @@ -49,6 +49,7 @@ background, and the intensity threshold for transition between them.

The default colour schemes are summarised in the table below:

 

+

Protein Colour Schemes

@@ -291,6 +292,81 @@ background, and the intensity threshold for transition between them.
+

 

+

Nucleotide Colour Schemes

+ + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
A C G T U I X R Y N W S M K B H D V
Nucleotide
Purine/Pyrimidine
+
+ +

 

diff --git a/help/html/colourSchemes/nucleotide.html b/help/html/colourSchemes/nucleotide.html index 8e2aa8b..9a62261 100755 --- a/help/html/colourSchemes/nucleotide.html +++ b/help/html/colourSchemes/nucleotide.html @@ -35,6 +35,7 @@ td { C G T + U diff --git a/help/html/colourSchemes/purinepyrimidine.html b/help/html/colourSchemes/purinepyrimidine.html new file mode 100644 index 0000000..373f0d0 --- /dev/null +++ b/help/html/colourSchemes/purinepyrimidine.html @@ -0,0 +1,40 @@ + + +Purine/Pyrimidine Colour Scheme + + + + +

Purine/Pyrimidine Colours

+
+ + + + + +
Purines
A, G, R		Pyrimidines
C, U, T, Y
+
+ + diff --git a/help/html/colourSchemes/rnahelicesColouring.html b/help/html/colourSchemes/rnahelicesColouring.html new file mode 100644 index 0000000..3034bf5 --- /dev/null +++ b/help/html/colourSchemes/rnahelicesColouring.html @@ -0,0 +1,50 @@ + + +RNA Helices Colouring + + +

RNA Helices Colouring

+

An RNA alignment loaded from a Stockholm file can be coloured + based on its helices. The helices are determined from the + secondary structure line in the Stockholm file (#GC SS_cons) + written in WUSS notation + that specifies base pairing. See + Wikipedia or + Jalview RNA Support Blog for more information about Stockholm files and WUSS notation.

+Select "Colour" → " + By RNA Helices" to colour the alignment by RNA helices.
+
+

Features

+
    +
  • Colours are generated randomly for the number of helices present. +Reselect the "By RNA Helices" option to generate another set of random colors.
    • +
  • Sequence logo is in +Purine/Pyrimidine colour scheme.
    • +
  • Line above the "Secondary Structure" line in annotation panel is WUSS notation present +in the input file.
    • +
+ + + +
+
+ + + + diff --git a/help/html/colourSchemes/rnahelicescoloring.png b/help/html/colourSchemes/rnahelicescoloring.png new file mode 100644 index 0000000..05e9230 Binary files /dev/null and b/help/html/colourSchemes/rnahelicescoloring.png differ diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html index c32d8fe..de9eac9 100755 --- a/help/html/features/seqfetch.html +++ b/help/html/features/seqfetch.html @@ -21,52 +21,33 @@

Sequence Fetcher

-

Jalview can retrieve sequences from certain databases using -either the WSDBFetch service provided by the European Bioinformatics -Institute, and, since Jalview 2.4, DAS servers capable of the sequence -command (configured in DAS settings).

-The Jalview Sequence Fetcher Dialog Box -

The Sequence Fetcher dialog box can be opened via the -"File" menu on the main desktop in order to retrieve sequences -as a new alignment, or opened via the "File" menu of an -existing alignment to import additional sequences. Please note, there -will be a short delay when the sequence fetcher is first opened, whilst -Jalview compiles the list of available sequence datasources from the -currently defined DAS server registry.

-

First, select the database you want to retrieve sequences from. -Then, enter one or more accession ids (as a semi-colon separated list), -or press the "Example" button to paste the example accession -for the currently selected database into the retrieval box. Finally, -press "OK" to initiate the retrieval.

-

Fetching Individual PDB Chains
-If you are retrieving sequences from the PDB, you can retrieve specific -chains by appending a colon and the chain id to the PDB id. For example -:
-

 1GAQ:A
-

-

Retrieving parts of large sequence records
-When retrieving from DAS sequence sources, coordinate range arguments -can be passed to the server using the standard DAS sequence command -format:

-  <AccessionId>:<start>,<end>
If you know a source -understands this type of query format, then you should untick the -checkbox for 'replace commas with semi-colons' so the range query can be -passed to the server; otherwise, the query will be split into two (e.g -'Mito:1' and '85779' rather than 'Mito:1,85779'). In most cases, -however, a source that supports range queries will include a range -qualification in its example query, and Jalview will then automatically -disable the 'replace commas with semi-colons' option.
-The option to disable the comma to semi-colon translation was -added in Jalview 2.6

-

If you use the WSDBFetch sequence fetcher services (EMBL, -Uniprot, PDB and PFAM) in work for publication, please cite:

-

Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., -Tate J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez -R.
-SOAP-based services provided by the European Bioinformatics Institute.
-Nucleic Acids Res. 33(1):W25-W28 (2005)
-
+

Jalview can retrieve sequences from certain databases using either the +WSDBFetch service provided by the European Bioinformatics Institute, and, since Jalview 2.4, DAS servers capable of the sequence command (configured in DAS settings).

+The Jalview Sequence Fetcher Dialog Box +

The Sequence Fetcher dialog box can be opened via the "File" + menu on the main desktop in order to retrieve sequences as a new + alignment, or opened via the "File" menu of an existing alignment + to import additional sequences. Please note, there will be a short delay when the sequence fetcher is first opened, + whilst Jalview compiles the list of available sequence datasources from the + currently defined DAS server registry.

+

First, select the database you want to retrieve sequences from. Then, enter + one or more accession ids (as a semi-colon separated list), or press the + "Example" button to paste the example accession for the currently selected database into the retrieval box. + Finally, press "OK" to initiate the retrieval.

+

+ If you are retrieving sequences from the PDB, you can retrieve + specific chains by appending a colon and the chain id to the PDB + id. For example :

 1GAQ:A

When retrieving from DAS sequence sources, + coordinate range arguments can be passed to the server using the standard DAS + sequence command format (:<start>,<end>)

+

If you use the WSDBFetch sequence fetcher services (EMBL, Uniprot, PDB, PFAM, and RFAM) + in work for publication, please cite:

+

Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate J., Velankar + S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez R.
+ SOAP-based services provided by the European Bioinformatics Institute.
+ Nucleic Acids Res. 33(1):W25-W28 (2005)
+
+

diff --git a/help/html/io/fileformats.html b/help/html/io/fileformats.html index f701dd0..228ae9a 100755 --- a/help/html/io/fileformats.html +++ b/help/html/io/fileformats.html @@ -63,6 +63,11 @@ THISISASEQENCE
PFAM SequenceName THISISASEQENCE .pfam + +Stockholm +# STOCKHOLM VersionNumber
+...
// +.stk, .sto

The file extensions are used to associate jalview alignment icons diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index 8156e93..5b6535d 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -26,7 +26,7 @@

  • Fetch Sequence
    Shows a dialog window in which you can select known ids from - Uniprot, EMBL, EMBLCDS or PDB database using Web Services provided by + Uniprot, EMBL, EMBLCDS, PDB, PFAM, or RFAM databases using Web Services provided by the European Bioinformatics Institute. See Sequence Fetcher.
  • Add Sequences
    @@ -361,7 +361,7 @@
  • Colour Scheme options: None, ClustalX, Blosum62 Score, Percentage Identity, Zappo, Taylor, Hydrophobicity, Helix Propensity, Strand Propensity, Turn Propensity, Buried Index, - Nucleotide, User Defined
    + Nucleotide, Purine/Pyrimidine, User Defined
     See colours for a description of all colour schemes.
    • @@ -387,6 +387,11 @@ annotation. See Annotation Colouring.
    +
  • By RNA Helices
    + Colours the helices of an RNA alignment loaded from a Stockholm file. See + RNA Helices + Colouring.
    +
  • Calculate diff --git a/help/html/menus/alwcolour.html b/help/html/menus/alwcolour.html index 10ec9c7..fa66701 100755 --- a/help/html/menus/alwcolour.html +++ b/help/html/menus/alwcolour.html @@ -31,7 +31,7 @@
  • Colour Scheme options: None, ClustalX, Blosum62 Score, Percentage Identity, Zappo, Taylor, Hydrophobicity, Helix Propensity, Strand Propensity, - Turn Propensity, Buried Index, Nucleotide, User Defined
    + Turn Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, User Defined
     See colours for a description of all colour schemes.
    • @@ -56,6 +56,11 @@ Colours the alignment on a per-column value from a specified annotation. See Annotation Colouring.
    +
  • By RNA Helices
    + Colours the helices of an RNA alignment loaded from a Stockholm file. See + RNA Helices + Colouring.
    +
    • diff --git a/help/html/menus/alwfile.html b/help/html/menus/alwfile.html index fd2ebe5..bf8ed9b 100755 --- a/help/html/menus/alwfile.html +++ b/help/html/menus/alwfile.html @@ -25,7 +25,7 @@

    Issues Resolved (a select list - see release