From 6368dda9a62fdc2e36b2b260666f093e9668dcad Mon Sep 17 00:00:00 2001 From: gmungoc Date: Fri, 2 Mar 2018 16:07:27 +0000 Subject: [PATCH] JAL-2729 draft help pages for HMMER menu --- help/help.jhm | 1 + help/helpTOC.xml | 1 + help/html/features/preferences.html | 16 +++++-- help/html/menus/alwhmmer.html | 87 +++++++++++++++++++++++++++++++++++ 4 files changed, 101 insertions(+), 4 deletions(-) create mode 100644 help/html/menus/alwhmmer.html diff --git a/help/help.jhm b/help/help.jhm index f129193..506b3f3 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -126,6 +126,7 @@ + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index 20dd8db..71b7ef9 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -152,6 +152,7 @@ + diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html index b29b66b..533af5c 100755 --- a/help/html/features/preferences.html +++ b/help/html/features/preferences.html @@ -62,8 +62,10 @@ sequence alignments and EPS files.
  • The "Editing" - Preferences tab contains settings affecting the export of - sequence alignments and EPS files. + Preferences tab contains settings affecting the behaviour of alignments as you edit them. +
    • +
  • The "HMMER" + Preferences tab allows you to configure locally installed HMMER tools.
  • The "DAS Settings" Preferences tab allows you to select which DAS @@ -387,7 +389,13 @@ Sort with New Tree - When selected, any trees calculated or loaded onto the alignment will automatically sort the alignment.

    -

     

    -

     

    +

    + "HMMER" Preferences tab +

    +

    If you have installed HMMER tools (available from hmmer.org), + then you should specify on this screen the location of the installation (the path to the folder + containing binary executable programs). Double-click in the input field to open a file browser.

    +

    When this path is configured, the HMMER menu will be + enabled in the Alignment window.

    diff --git a/help/html/menus/alwhmmer.html b/help/html/menus/alwhmmer.html new file mode 100644 index 0000000..ce23c4b --- /dev/null +++ b/help/html/menus/alwhmmer.html @@ -0,0 +1,87 @@ + + + + + +

    + HMMER Menu +

    +

    This menu is available if hmmbuild tools have been installed and configured in the +HMMER Preferences panel. +

    + + hmmbuild +

    Run hmmbuild to create a Hidden Markov Model profile of your sequence alignment or sub-groups. +

    The consensus sequence for the computed profile is inserted as the first sequence of + the alignment (or group) for which hmmbuild is run. +
    Jalview also computes and displays an annotation below the alignment, showing + the information content of each column. +
    This is calculated as the sum over residue symbols of + 

    +    match emission probability * log(match emission probability / background frequency) / log(2)
+
    + where the background frequencies are taken from (tbc: where? not https://www.ebi.ac.uk/uniprot/TrEMBLstats) +
      +
    • Edit settings and run... +

      Choose whether to run hmmbuild for the whole alignment, or all or selected groups, or both + (default is the alignment). +
      Optionally enter a name to give the HMM profile consensus sequence + (default is "Alignment" or group name, with "_HMM" appended). +
      Use Reference Annotation: select this option if your alignment has an RF reference annotation, + and you wish to constrain the HMM profile to it (hmmbuild option '--hand'). +

      • +
    • hmmbuild with default settings +

      Runs hmmbuild for the whole alignment.
      • +
    + + hmmalign and hmmsearch require an HMM consensus sequence to be selected first. +
    To do this, right-click on the name of an HMM sequence added by hmmbuild, and 'Select HMM'. + The alignment will be with respect to the HMM profile for the consensus sequence. +

    + hmmalign +

    Run hmmalign to align selected sequences (or the whole alignment) to a selected HMM profile. +
      +
    • Edit settings and run... +

      Choose whether to 'trim non-matching termini' - hmmalign option '--trim'. +

      • +
    • hmmalign with default settings
      • +
    + hmmsearch +

    Run hmmsearch to use an HMM profile as input to search a sequence database. +
      +
    • Edit settings and run... +
        +
      • tbc: choose database
        • +
      • tbc: automatically align
        • +
      • tbc: return accessions
        • +
      • tbc: number of results
        • +
      • tbc: sequence eValue cutoff
        • +
      • tbc: domains eValue cutoff
        • +
      +
      • +
    • hmmsearch with default settings
      • +
    • Add database +
      Browse to select a local sequence data file to be searched
      • +
    +
    + + -- 1.7.10.2