Fix the reference genome to compare

[shashibisht9]

Hi,

I would like to compare the Blast Score Ratio (BSR) of a single reference genome against 10 closely related genomes using their NCBI annotated locus_tags. Currently, when I run the ls_bsr.py script, the reference genome is switching among all the genomes I want to compare. I need help to fix the reference genome and obtain the BSR for the rest of the genomes in comparison. Furthermore, I would like to export the Kegg annotations of each compared gene to an Excel file.

Thank you so much!

[jasonsahl]

So if you have a set of annotated locus tags, you can provide these as input via the "-g" flag. The resulting BSR matrix will show the BSR values across all genomes for each feature in your sequences provided with "-g". Does that work? As for the Kegg annotations, if they are in the locus header, you can extract them easily, but there is currently no Kegg support in LS-BSR.

[shashibisht9]

Hi,

Yes, it worked giving input fasta file having annotated locus tags with -g. Thank you so much for your support.