I have a tab-delimited list with genomic mutations of Drosophila melanogaster mapped to FlyBase r5.50 genome assembly. List contains such fields as gene name, chromosome, strand, genomic coordinates, original allele and mutated allele. Are there software or on-line server to convert these mutations in the changes in the protein sequence or aminoacid changes with positions in the protein?
Maybe you want to look at Anovar, that predicts non synonymous snps. There is a great list of tools for Human, so maybe you can adopt some. Especially since Dros is also one very commonly studied organism.
Good Luck
SNPeff could be one tool to use this. However the fields which are required in that is little bit different.
Hi,
I can't suggest a specific tool. But, I suggest this site:
http://usegalaxy.org/
There are quite a lot of tools.... Hope it's useful for you.
Regards,
Thanks guys! Very useful software, but I decided to construct my own pipeline. It involves ready to use tools from FlyBase and UCSC Genome Browser and several simple Python scripts to create inputs and parse outputs.
Hi Dimitry,
I have to say, It's a very good idea..... Well me too, I have done my pipeline with Python and bash.
Regards,
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