genomic co-ordinate, map

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4.3 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

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ADD COMMENT • link 4.3 years ago by mdfardin374 ▴ 10

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Have you considered the possibility that there is no hit for those peptides in whatever database you used for your search?

ADD REPLY • link 4.3 years ago by GenoMax 141k

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Yes I have considered the possibility of "hit"; almost every peptide has hit in the database

ADD REPLY • link 4.3 years ago by mdfardin374 ▴ 10

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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.

ADD REPLY • link 4.3 years ago by ATpoint 81k

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Its genomic DNA database but in case of exon/exon boundaries it can show the span region.

ADD REPLY • link 4.3 years ago by mdfardin374 ▴ 10

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