blastxml-0.3.2: Library for reading Blast XML output

Safe HaskellNone
LanguageHaskell98

Bio.BlastData

Description

This module implements a hierarchical data structure for BLAST results.

BLAST is a tool for searching in (biological) sequences for similarity. This library is tested against NCBI-blast version 2.2.14. There exist several independent versions of BLAST, so expect some incompatbilities if you're using a different BLAST version.

For parsing BLAST results, the XML format (blastall -m 7) is by far the most robust choice, and is implemented in the Bio.Alignment.BlastXML module.

The format is straightforward (and non-recursive). For more information on BLAST, check http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/information3.html

Synopsis

Documentation

data Aux #

The Aux field in the BLAST output includes match information that depends on the BLAST flavor (blastn, blastx, or blastp). This data structure captures those variations.

Constructors

Strands !Strand !Strand

blastn

Frame !Strand !Int

blastx

Instances

Eq Aux # 

Methods

(==) :: Aux -> Aux -> Bool #

(/=) :: Aux -> Aux -> Bool #

Show Aux # 

Methods

showsPrec :: Int -> Aux -> ShowS #

show :: Aux -> String #

showList :: [Aux] -> ShowS #

data BlastRecord #

Each query sequence generates a BlastRecord

Constructors

BlastRecord 

Fields

data BlastHit #

Each match between a query and a target sequence (or subject) is a BlastHit.

Constructors

BlastHit 

Instances

data BlastMatch #

A BlastHit may contain multiple separate matches (typcially when an indel causes a frameshift that blastx is unable to bridge).

Constructors

BlastMatch 

Fields