Description

This track shows the blat alignment of protein sequences from other strains to this reference sequence: ASM1346v1/USA300_FPR3757. It shows the alignments of the protein sequences of each of the other strains mapped against this reference strain. The results are separated into different tracks, based on the percent match to the reference. A click into any item gives access to the pairwise alignment between the selected strain and the reference.

Methods

The blat procedure was operated via the gfServer/gfClient system where the gfServer service was started:

   gfServer start <serverName> 17897 -stepSize=5 staAur2.2bit
and
   gfServer start <serverName> 17896 -trans -mask staAur2.2bit
And the gfClient command is directed to the translated server, and is operated simply:
   gfClient -t=dnax -q=prot <serverName> 17896 . <query.faa> <result.psl>

The other strain protein sequences are obtained from their NCBI RefSeq release as supplied in the release .gff.gz file.

References

Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64.