get genomic information for probe sequence

Question

[biotechdiya]

Hi,

i have few probe sequences and I need their genomic coordinates,mrna positions. I have the refseq file from ucsc and build.fa. will these be sufficient to get the information that i am looking for?

Thanks,

[GenoMax]

You could simply blat the sequences at UCSC if your genome is available there.

[biotechdiya]

thank you. That gives me genomic positions. How about to get cds start txstart gene name details etc? Should I go another query with the genomic positions that I get from the blat db?

[Biological information research group o…]

I have another idea that I hope can help you.Sequence alignment was made with fa file and probe sequence of reference genome sequence and mrna reference sequence respectively, and then python code was written to extract location information from alignment result XML or other format files.The probe sequence also needs to be fa formatted. If the probe sequence is small enough, blast can be used online.