Question: How to extract the coordinates for the BRCT domain (BRCA1) nucleotide sequence?
0
gravatar for bioinfo89
2.3 years ago by
bioinfo8940
bioinfo8940 wrote:

Hi all,

I am working on breast cancer data. I have protein sequence for BRCT domain and I want know its nucleotide sequence coordinates. I tried using tblastn to get the corresponding nucleotide sequence (~294bp) and then I used ensemble blast to get the coordinates of the nucleotide sequence obtained from tblastn, but the blast result shows very less query length (<100 bps) mapping to BRCA1 regions.

I am not sure if the approach I am using is completely correct therefore any suggestions will be helpful.

Thanks!

sequence • 658 views
ADD COMMENTlink written 2.3 years ago by bioinfo8940

Shouldn't tblastn give you the genomic coordinates directly?

fin swimmer

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by finswimmer13k

No it gives the corresponding nucleotide sequence (known Genbank accession ID).

ADD REPLYlink written 2.3 years ago by bioinfo8940

Hm, if I use tblastn from Ensembl or UCSC I'll get genomic coordinates.

ADD REPLYlink written 2.3 years ago by finswimmer13k

Blastn from Ensembl!

ADD REPLYlink written 2.3 years ago by bioinfo8940

???

Blastn from Ensembl gave you the result you need? Or did you used it before and the result was not as expected?

ADD REPLYlink written 2.3 years ago by finswimmer13k

I used it to get the result. But the mapped regions were scattered. (eg. 1 to 63 of the query mapped to different coordinate, 64 to 123 mapped to different coordinate etc).

ADD REPLYlink written 2.3 years ago by bioinfo8940

Do you have a link for the protein sequence for BRCT ? If yes, then do share!

ADD REPLYlink written 2.3 years ago by lakhujanivijay5.2k
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