| Safe Haskell | None |
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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 {
- blastprogram :: !ByteString
- blastversion :: !ByteString
- blastdate :: !ByteString
- blastreferences :: !ByteString
- database :: !ByteString
- dbsequences :: !Integer
- dbchars :: !Integer
- results :: [BlastRecord]
- data BlastRecord = BlastRecord {}
- data BlastHit = BlastHit {}
- 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 Source
A BlastResult is the root of the hierarchy.
Constructors
| BlastResult | |
Fields
| |
Instances
| Show BlastResult |
Each match between a query and a target sequence (or subject)
is a BlastHit.
Constructors
| BlastHit | |
Instances
| Show BlastHit |
data BlastMatch Source
A BlastHit may contain multiple separate matches (typcially when
an indel causes a frameshift that blastx is unable to bridge).
Constructors
| BlastMatch | |
Instances
| Show BlastMatch |