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How to extract the coordinates for the BRCT domain (BRCA1) nucleotide sequence?

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
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written by bioinfo89 • bioinfo89

Shouldn't tblastn give you the genomic coordinates directly?

fin swimmer

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written by finswimmer finswimmer

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

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written by bioinfo89 • bioinfo89

???

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

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written by finswimmer finswimmer

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).

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written by bioinfo89 • bioinfo89

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

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written by lakhujanivijay lakhujanivijay

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