Mapping ORFs to Chromosome locations

Question

[arkajyoti.ghoshal]

Hi, I have a list of ORFs with their chromosome number and start and stop nucleotide sequences. I was wondering that, given a set of genes (w/ start and stop seq and chromosome no.), can I use any tool that can map these orfs to chromosome sequence and see if they fall within or outside this region!!

Answer 1

[Vivek]

You can align the sequences using BLAT.

https://genome.ucsc.edu/cgi-bin/hgBlat?command=start

Convert the top alignments from the resulting PSL file to BED format and use BEDtools to check the intersection with your coordinates.

[arkajyoti.ghoshal]

Thanks Vivek. will try that.