Entering edit mode
6.5 years ago
bioinfo89
▴
60
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!
Shouldn't tblastn give you the genomic coordinates directly?
fin swimmer
No it gives the corresponding nucleotide sequence (known Genbank accession ID).
Hm, if I use tblastn from Ensembl or UCSC I'll get genomic coordinates.
Blastn from Ensembl!
???
Blastn from Ensembl gave you the result you need? Or did you used it before and the result was not as expected?
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).
Do you have a link for the protein sequence for BRCT ? If yes, then do share!