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

  1. Query id
  2. Subject id
  3.  % identity
  4. alignment length
  5. mismatches
  6. gap openings
  7. q. start
  8. q. end
  9. s. start
  10. s. end
  11. e-value
  12. 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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