Large scale Blast Score Ratio (BSR) analysis
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ls_bsr
test_data
tests
tools
LS_BSR_manual.pdf
README.md
_config.yml
changelog.md
igs_logging.py
license.txt
ls_bsr.py
manual.md
setup.py

README.md

LS-BSR (Large Scale Blast Score Ratio) is released under the GPL version 3 license. See "license.txt" for more information

LS-BSR is a method to compare all coding regions in a large set of genomes. Each peptide is compared against it's nucleotide sequence in order to obtain the maximum BLAST bit score. Each peptide is then aligned against each genome in order to find the query BLAST bit score. The query dividied by the reference provides one with the BSR, which can range from 0 to 1; scores slightly higher than 1.0 can be observed due to variable bit scores obtained by BLAST. In my opinion, they should be treated as 1.0. Due to the "-C F" flag added recently, values > 1.00 have not been observed.

contact: jasonsahl at gmail dot com

Minimum requirements, see manual.md for version information

  1. Python >2.7 and <=3.5
  2. BioPython
  3. Prodigal - Required for de novo gene prediction only
  4. VSEARCH - Optional
  5. USEARCH - Optional
  6. CD-HIT - Optional
  7. Blast+ - Optional
  8. Blat - Optional
  9. Diamond - Optional

*See changelog.md for a list of changes
*See manual.md for run directions