Question: Get positions from FASTA alignment in bed format
0
gravatar for kalahari
8 months ago by
kalahari0
kalahari0 wrote:

Hello, I have created multiple species aligments and I have found regions of interests in these alignments. They are certain aminoacids in the alignments that I have extracted based on the human position.

>human
GMRGGVATSCHVAW
>mouse
GMRGGVATSMHVAW

Interest regions: Human, position 9, "C"

I would like to obtain the bed coordinates (in hg19) for these positions but I am not too sure how to "map" my protein alignments to the hg19 genome and then add my positions (based in my original alignment) to get their localization in bed format. Could anyone suggest me an approach to perform this? Thank you very much.

bam alignment bed fasta • 282 views
ADD COMMENTlink written 8 months ago by kalahari0

Do you have more information about these protein sequences, like transcript or gene?

ADD REPLYlink written 8 months ago by finswimmer12k
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