| Safe Haskell | None |
|---|---|
| Language | Haskell98 |
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
- data Aux
- data BlastResult = BlastResult {}
- data BlastRecord = BlastRecord {}
- data BlastHit = BlastHit {
- hitId :: !ByteString
- subject :: !SeqLabel
- slength :: !Int
- matches :: [BlastMatch]
- data BlastMatch = BlastMatch {}
Documentation
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.
data BlastResult #
A BlastResult is the root of the hierarchy.
Constructors
| BlastResult | |
Fields
| |
Instances
Each match between a query and a target sequence (or subject)
is a BlastHit.
Constructors
| BlastHit | |
Fields
| |
data BlastMatch #
A BlastHit may contain multiple separate matches (typcially when
an indel causes a frameshift that blastx is unable to bridge).
Constructors
| BlastMatch | |
Instances