Difference between revisions of "Blast"
| Line 9: | Line 9: | ||
This is for the old blast and mpiblast | 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 17:18, 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
