X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=5f60ba52d6323b95055ab6742350fe4fc583404d;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=427ab2d592a782f6e34c11f9ad1ec7b32b14fc9c;hpb=b64d78cc81a4d3f87ac03b4f530757b840c4f943;p=jalview.git diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index 427ab2d..5f60ba5 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -1,365 +1,678 @@ - -Alignment Window Menus - - -

Alignment Window Menus

- - - + + + +Alignment Window Menus + + + + +

+ Alignment Window Menus +

+ + + +
  • Colour +
      +
    • Apply Colour To All Groups
      +       If this is selected, any changes made to the background + colour will be applied to all currently defined groups.
      +
      • +
    • Colour Text...
      Opens the Colour Text + dialog box to set a different text colour for light and dark + background, and the intensity threshold for transition between + them.
      • +
    • Colour Scheme options: None, ClustalX, + Blosum62 Score, Percentage Identity, Zappo, Taylor, + Hydrophobicity, Helix Propensity, Strand Propensity, Turn + Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, User + Defined
      +       See colours + for a description of all colour schemes. +
      • +
    • By Conservation
      +       See Colouring + by Conservation. +
      • +
    • Modify Conservation Threshold
      +       Use this to display the conservation threshold slider + window. Useful if the window has been closed, or if the 'by + conservation' option appears to be doing nothing!
      • +
    • Above Identity Threshold
      +       See Above + Percentage Identity + .
      +
      • +
    • Modify Identity Threshold
      +       Use this to set the threshold value for colouring above + Identity. Useful if the window has been closed.
      +
      • +
    • By Annotation
      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. +
      • +
    • +
  • Calculate +
      +
    • Sort +
        +
      • by ID
        This will + sort the sequences according to sequence name. If the sort + is repeated, the order of the sorted sequences will be + inverted.
        • +
      • by Length
        This + will sort the sequences according to their length + (excluding gap characters). If the sort is repeated, the + order of the sorted sequences will be inverted.
        • +
      • by Group
        This + will sort the sequences according to sequence name. If the + sort is repeated, the order of the sorted sequences will + be inverted.
        • +
      • by Pairwise Identity
        +         This will sort the selected sequences by their + percentage identity to the consensus sequence. The most + similar sequence is put at the top.
        • +
      • The Sort + menu will have some additional options if you have just + done a multiple alignment calculation, or opened a tree + viewer window. +
        • +
      • +
    • Calculate Tree
      Functions + for calculating trees on the alignment or the currently + selected region. See calculating + trees. + +
        +
      • Neighbour Joining Using PAM250
        • +
      • Neighbour Joining Using Sequence + Feature Similarity
        • +
      • Neighbour Joining Using Blosum62
        • +
      • Neighbour Joining Using % Identity
        • +
      • Average Distance Using PAM250
        • +
      • Average Distance Using Sequence + Feature Similarity
        • +
      • Average Distance Using Blosum62
        • +
      • Average Distance Using % Identity
        • +
      Note: Since Version 2.8.1, a number of + additional similarity measures for tree calculation are + provided in this menu.
      • +
    • Pairwise Alignments
      Applies + Smith and Waterman algorithm to selected sequences. See pairwise alignments. +
      • +
    • Principal Component Analysis
      Shows + a spatial clustering of the sequences based on similarity + scores calculated with the alignment. See Principal Component Analysis. +
      • +
    • Extract Scores ... (optional)
      This + option is only visible if Jalview detects one or more + white-space separated values in the description line of the + alignment sequences.
      When selected, these numbers are + parsed into sequence associated annotation which can then be + used to sort the alignment via the Sort by→Score menu. +
      • +
    • Autocalculate Consensus
      For + large alignments it can be useful to deselect + "Autocalculate Consensus" when editing. This + prevents the sometimes lengthy calculations performed after + each sequence edit.
      • +
    • Sort With New Tree
      When + enabled, Jalview will automatically sort the alignment when a + new tree is calculated or loaded onto it.
      • +
    • Show Flanking Regions
      Opens + a new alignment window showing any additional sequence data + either side of the current alignment. Useful in conjunction + with 'Fetch Database References' when the 'Trim Retrieved + Sequences' option is disabled to retrieve full length + sequences for a set of aligned peptides.
      • +
    • + +
  • Web Service Menu
    This menu + is dynamic, and may contain user-defined web service entries in + addition to any of the following ones: +
      +
    • Fetch DB References
      This + submenu contains options for accessing any of the database + services that Jalview is aware of (e.g. DAS sequence servers + and the WSDBFetch service provided by the EBI) to verify + sequence start/end positions and retrieve all database cross + references and PDB ids associated with all or just the + selected sequences in the alignment. +
        +
      • 'Trim Retrieved Sequences' - when checked, Jalview + will discard any additional sequence data for accessions + associated with sequences in the alignment.
        Note: + Disabling this could cause out of memory errors when + working with genomic sequence records !
        Added + in Jalview 2.8.1 +
        • +
      • 'Standard Databases' will check sequences against + the EBI databases plus any active DAS sequence sources<
        • +
      Other sub-menus allow you to pick a specific source to query + - sources are listed alphabetically according to their + nickname. +
      • +
    +

    Selecting items from the following submenus will start a + remote service on compute facilities at the University of Dundee, + or elsewhere. You need a continuous network connection in order to + use these services through Jalview.

    +
      +
    • Alignment
      + Align the currently selected sequences or all sequences + in the alignment, or re-align unaligned sequences to the + aligned sequences. Entries in this menu provide access to the + various alignment programs supported by JABAWS. See the Multiple + Sequence Alignment webservice client entry for more + information. +
      • +
    • Secondary Structure Prediction +
        +
      • JPred Secondary Structure Prediction
        + Secondary structure prediction by network + consensus. See the Jpred3 + client entry for more information. The behaviour of this + calculation depends on the current selection: +
          +
        • If nothing is selected, and the displayed + sequences appear to be aligned, then a JNet prediction + will be run for the first sequence in the alignment, + using the current alignment. Otherwise the first + sequence will be submitted for prediction.
          • +
        • If just one sequence (or a region on one + sequence) has been selected, it will be submitted to + the automatic JNet prediction server for homolog + detection and prediction.
          • +
        • If a set of sequences are selected, and they + appear to be aligned, then the alignment will be used + for a Jnet prediction on the first + sequence in the set (that is, the one that appears + first in the alignment window). +
          • +
        +         +
      • +
    • Analysis
      +
        +
      • Multi-Harmony
        Performs + functional residue analysis on a protein family alignment + with sub-families defined on it. See the Multi-Harmony service entry for more information. +
        • +
      • +
    • + + + +