# Package org.snpeff.nextProt

package org.snpeff.nextProt

Related Packages
Package
Description
org.snpeff
Classes
Class
Description
CvTerm
A controlled vocabulary term
Location
A location (i.e.
LocationTargetIsoform
A location respect to an isoform
LocationTargetIsoformInteraction
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.
NextProtDb
Parse NetxProt XML file and build a database
NextProtHandler
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/
NextProtMarkerFactory
Creates Markers from nextprot XML annotations
NextProtSequenceConservation
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.
NextProtXmlAnnotation
Mimics the 'annotation' tag in a NextProt XML file
NextProtXmlEntry
Mimics the 'entry' in a NextProt XML file
NextProtXmlIsoform
Mimics the 'isoform-mapping' in a NextProt XML file
NextProtXmlNode
Mimics a node in NextProt XML file