blast

Basic Local Alignment Tool

Wraps BLAST [[Alt90]], probably the most popular similarity search tool in bioinformatics.

Commands

clean
Remove all job data, not the Moa job itself, note that this must be implemented by the template.
report
Generate a text BLAST report.
run
Running BLAST takes an input directory, determines what sequences are present and executes BLAST on each of these. Moa BLAST is configured to create XML output (as opposed to the standard text based output) in the out directory. The output XML is subsequently converted to GFF3 by the custom blast2gff script (using BioPython). Additionally, a simple text report is created.

Filesets

db

Blast database

type: single
category: prerequisite
optional: False
pattern: */*
input
Directory with the input files for BLAST, in Fasta format
outgff

GFF output files

type: map
source: input
category: output
optional: True
pattern: gff/*.gff
output

XML blast output files

type: map
source: input
category: output
optional: True
pattern: out/*.out

Parameters

eval

e value cutoff

type: float
default: 1e-10
optional: True
gff_blasthit

(T,**F**) - export an extra blasthit feature to the created gff, grouping all hsp (match) features.

type: set
default: F
optional: True
gff_source

source field to use in the gff

type: string
default: BLAST
optional: True
nohits

number of hits to report

type: integer
default: 50
optional: True
nothreads

threads to run blast with (note the overlap with the Make -j parameter)

type: integer
default: 2
optional: True
program

blast program to use (default: blastn)

type: set
default: blastn
optional: True

miscellaneous

Backend
ruff
Author
Mark Fiers
Creation date
Wed Nov 10 07:56:48 2010
Modification date
Wed Nov 10 07:56:48 2010