Entering edit mode
4.9 years ago
mdfardin374
▴
10
Hello, I have 1200 peptide sequence in a fasta file and I want to know their genomic co-ordinate so I run blastx on command line. I have not been able to get genomic co-ordinate for all peptide. Please help me
Have you considered the possibility that there is no
hitfor those peptides in whatever database you used for your search?Yes I have considered the possibility of "hit"; almost every peptide has hit in the database
What is the database you used? I would use a collection of cDNAs for that since genomic coordinates can be difficult once the CDS spans exon/exon boundaries.
Its genomic DNA database but in case of exon/exon boundaries it can show the span region.