Fetch The Location And Nucleotide Sequence Through Webservice For Drosophila Melanogaster

Question

[abuzarhamza]

I have the list of gene (huge number), and want to fetch the gene position from the genome Drosophila melanogaster along with nucleotide sequence eg bi Pph13 abd-A peb Gsc Abd-B

I need the wsdl of such service along the call

Or some other way to fetch the record

[Josh Herr]

What have you tried so far?

It's very important to make sure you know how to spell the organism you are working with. When I see mistakes in the spelling of your model organism I automatically assume there will be mistakes in all other areas of your science.

Answer 1

[Raygozak]

If you have the fasta reference sequence and gff anotation for your organism, you can use the fastahack library (github) to fetch the sequences based on the positions defined for a specific gene in the gff file. for the position you can try doing a grep in your anotation file and automate all this using a shell script.

note that the fastahack code compiles a command line utility for you without the need for you to redo it if you don't want to actually code in c++.