Question: Mapping ORFs to Chromosome locations
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gravatar for arkajyoti.ghoshal
3.2 years ago by
arkajyoti.ghoshal0 wrote:

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!!

mapping orfs genome • 885 views
ADD COMMENTlink modified 3.2 years ago by Vivek2.4k • written 3.2 years ago by arkajyoti.ghoshal0
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gravatar for Vivek
3.2 years ago by
Vivek2.4k
Denmark
Vivek2.4k wrote:

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.

ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by Vivek2.4k

Thanks Vivek. will try that.

ADD REPLYlink written 3.2 years ago by arkajyoti.ghoshal0
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