From 11d7be472ca5ea89d69e5bb7882c0058b2c3c4b9 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Wed, 9 Sep 2015 17:07:09 +0100 Subject: [PATCH] JAL-1645 update 2.9 docs --- help/html/features/seqfetch.html | 43 ++++++++++------- help/html/features/splitView.html | 94 +++++++++++++++++++++++++++---------- help/html/releases.html | 85 ++++++++++++++++++--------------- help/html/whatsNew.html | 7 ++- 4 files changed, 142 insertions(+), 87 deletions(-) diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html index 2a7c429..89b3d3b 100755 --- a/help/html/features/seqfetch.html +++ b/help/html/features/seqfetch.html @@ -25,7 +25,7 @@

Sequence Fetcher

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

+DBFetch service provided by the EMBL European Bioinformatics Institute, or, 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" @@ -35,7 +35,7 @@ WSDBFetch service provided by the European Bioinformatics Institute, or, since J 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 +

First, select the database you want to retrieve sequences from by clicking the button labeled 'Select database retrieval source'. If a database source is already selected, then the button's label will change to show the currently selected database.

@@ -45,25 +45,32 @@ WSDBFetch service provided by the European Bioinformatics Institute, or, since J databases are ordered alphabetically, and if there are many sources for the same type of sequence identifier, they will be grouped together in a sub-branch branch labeled with the identifier.

-

Once you have selected the sequence database using the popup dialog box, enter - one or more accession ids (as a semi-colon separated list), or press the +

Once you have selected the sequence database using the popup dialog box, 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.

-

Since Jalview 2.9 if PDB is selected as the sequence database, a specialised interface - PDB Sequence Fetcher is used for discovering and retrieving the sequence data.

-

Specifying chains for PDB IDs - 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
+

+ Fetching from The PDB with the EMBL-EBI PDBe Search + Interface

-

- Only retrieving part of a sequence DAS sources - (indicated by a "(DAS)") allow a range to be - specified in addition to a sequence ID. To retrieve 50 residues - starting at position 35 in UNIPROT sequence P73137 using the UNIPROT - DAS server, you would enter "'P73137:35,84'.
Full support for DAS range queries was introduced in Jalview 2.8 -

- -

If you use the WSDBFetch sequence fetcher services (EMBL, Uniprot, PDB, PFAM, and RFAM) +

+ Since Jalview 2.9, selecting PDB as the sequence database will open + the PDB Sequence Fetcher for + discovering and retrieving structures. +

+

+ Only retrieving part of a sequence +

+

+ DAS sources (indicated by a "(DAS)") allow a + range to be specified in addition to a sequence ID. To retrieve 50 + residues starting at position 35 in UNIPROT sequence P73137 using + the UNIPROT DAS server, you would enter "'P73137:35,84'.
+ Full support for DAS range queries was introduced in + Jalview 2.8 +

+ +

If you use the WSDBFetch sequence fetcher services (EMBL, Uniprot, 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.
diff --git a/help/html/features/splitView.html b/help/html/features/splitView.html index 59894f6..caf8cd4 100644 --- a/help/html/features/splitView.html +++ b/help/html/features/splitView.html @@ -24,25 +24,64 @@

Split Frame Views

-

Coding DNA (cDNA) and its protein product can be displayed in a split view, with cDNA above and protein below. The two alignments are -linked, with these features supported: - -

An alignment annotation row on the protein alignment shows the cDNA consensus for each peptide column.
+

+ Jalview provides a special viewing mode to show Coding DNA (cDNA) + and protein product alignments as a split view, with cDNA above and + protein below. The two alignments are linked, allowing editing and + analysis to be performed at both the peptide and nucleotide level. + Linked protein alignments also have an additional + cDNA Consensus annotation row, showing the + distribution of codons at each column + of the protein alignment. +

+

+ Split Frame views can be created in a number of ways. In the Jalview + Desktop, Split Frame views are saved in Jalview Projects, like any + other alignment view. +

+

Operations supported in Split Frame Mode

+

Split Frame views allow the following: + +

+

An alignment annotation row on the protein alignment shows the cDNA consensus for each peptide column.
This consensus may reveal variation in nucleotides coding for conserved protein residues.

-

Opening a Split Frame View

+

Opening a Split Frame View

A Split Frame View can be opened in one of the following ways:

Add Sequences

If you add (coding) DNA sequences to an open peptide alignment, or vice versa, and at least one DNA sequence translates to one of the @@ -72,15 +111,18 @@ On selecting protein cross-references (for a cDNA alignment), or DNA xrefs (for

  • Jalview reconstructs the alignment of its complement (in this case, cDNA) by inserting gaps in the corresponding positions
    • -

    Reconstructed Alignments - Reconstructed alignments are typically not - the same as the alignment produced by aligning the complement - sequence set directly with the external service. However, in the - case of protein alignments, a reconstructed cDNA alignment is often - more reliable than one calculated without coding information. - Reconstructed cDNA alignments are also more informative than the - original protein alignment when calculating phylogenetic trees or - performing other kinds of molecular evolution analysis. +

    + Reconstructed Alignments +

    +

    + Reconstructed alignments are typically not the same as the + alignment produced by aligning the complement sequence set directly + with the external service. However, in the case of protein + alignments, a reconstructed cDNA alignment is often more reliable + than one calculated without coding information. Reconstructed cDNA + alignments are also more informative than the original protein + alignment when calculating phylogenetic trees or performing other + kinds of molecular evolution analysis.

    Split Frame Views were introduced in Jalview 2.9 diff --git a/help/html/releases.html b/help/html/releases.html index f8b6d29..d9a9304 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -62,25 +62,20 @@

  • Jmol integration updated to Jmol v14.2.14
    • -
  • Import and export of Jalview alignment views as BioJSON
    • +
  • Import and export of Jalview alignment views as BioJSON
  • New alignment annotation file statements for reference sequences and marking hidden columns
    • -
  • Assign an alignment reference sequence to highlight - variation
    • +
  • Reference sequence based alignment shading to + highlight variation
  • Select or hide columns according to alignment annotation
    • -
  • Find option for locating sequences by - description
    • +
  • Find option for locating sequences by description
  • Conserved physicochemical properties shown in amino acid conservation row
  • Alignments can be sorted by number of RNA helices
    • - - Application + Application