Blast

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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
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