Here's the specifics: I have a GenBank ID and a coordinate (M61857.1:1144). I would like to convert it to a coordinate in a reference sequence (e.g. NM_123456.1:789). Is there a web service or tool that can do this? If not, what's the easiest way to do this through web tools?
As background, I have used NCBI's blast tool on M61857.1 and I get an alignment to NM_000771.3. It's a good match but I would like to take it a step further and somehow enter the coordinate 1144 and get back a coordinate for NM_000771.3. It also shows a good visual alignment I know I can go through the alignment output on the result page and count by hand but that is extremely inefficient and prone to error.
UCSC has the similar BLAT tool that gives similar output where I have to follow the alignment by hand and count bases.
Ultimately I want to be able to do this for a whole bunch of different positions and GenBank IDs so finding a web service that could do this would be a godsend.
I'm not a trained bioinformatician so please forgive if this is a dumb question.
so...to make sure I got it right, you want to enter a nucleotide position (i.e. 1144) and get as a result the ID that matches with M61857.1 from that position to the end of the sequence?
Not really, but thanks for clarifying. I want to give, as input, the sequence ID and position M61857.1:1144 and then get back the corresponding position on the reference sequence (which should look something like NM_123456.1:789). Does that make sense? Given a position on one sequence (possibly non-reference), give me the equivalent position on the reference sequence.