Difference between revisions of "Blast"
| Line 1: | Line 1: | ||
=Introduction= | =Introduction= | ||
| + | |||
The workhorse of bioinformatics, some tips on usage, and (mostly) how to speed it up | The workhorse of bioinformatics, some tips on usage, and (mostly) how to speed it up | ||
| + | |||
| + | = Output formats = | ||
| + | |||
| + | == -m 9 == | ||
| + | |||
| + | This is for the old blast and mpiblast | ||
| + | |||
| + | * Query id | ||
| + | * Subject id | ||
| + | * % identity | ||
| + | * alignment length | ||
| + | * mismatches | ||
| + | * gap openings | ||
| + | * q. start | ||
| + | * q. end | ||
| + | * s. start | ||
| + | * s. end | ||
| + | * e-value | ||
| + | * bit score | ||
= Benchmark Exercises = | = Benchmark Exercises = | ||
Revision as of 16:17, 1 February 2016
Contents
Introduction
The workhorse of bioinformatics, some tips on usage, and (mostly) how to speed it up
Output formats
-m 9
This is for the old blast and mpiblast
- Query id
- Subject id
- % identity
- alignment length
- mismatches
- gap openings
- q. start
- q. end
- s. start
- s. end
- e-value
- bit score
Benchmark Exercises
Transcriptome Panda Blood
- 92600 transcripts (contigs) in 2.4 million line FASTA file.
- blastx speed on 62-fragmented nr database: 5% (about 4500 contigs then) in 33 hours on blastx
