Package org.snpeff.nextProt


package org.snpeff.nextProt
  • Classes
    Class
    Description
    A controlled vocabulary term
    A location (i.e.
    A location respect to an isoform
    A location respect to two locations within an isoform In this case "start" and "end" are not really an interval, but an interaction between two locations (e.g.
    Parse NetxProt XML file and build a database
    Handler used in XML parsing for NextProt database It keeps track of the tags and saves state data to create Markers using NextProtMarkerFactory http://www.nextprot.org/
    Creates Markers from nextprot XML annotations
    A simple analysis of sequence conservation for each entry type Why? Many NextProt annotations are only a few amino acids long (or only 1 AA) and often they only involve very specific sequences If the sequence is highly conserved and a non-synonymous mutation occurs, then this might be disruptive (i.e.
    Mimics the 'annotation' tag in a NextProt XML file
    Mimics the 'entry' in a NextProt XML file
    Mimics the 'isoform-mapping' in a NextProt XML file
    Mimics a node in NextProt XML file