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Fetch The Location And Nucleotide Sequence Through Webservice For Drosophila Melanogaster

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

webservice gene
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updated by Raygozak Raygozak • written by abuzarhamza • abuzarhamza

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.

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written by Josh Herr Josh Herr

1 answer

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++.

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written by Raygozak Raygozak

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