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relf20 10-21-2010 10:01 PM

issues with homologous genes and bioinformatics

Sorry for what is going to be a bit of a rambly problem!

I'm looking for Potato genes which are homolgous to a family of genes in Arabidopsis, the sequences of which are all pretty similar. The Potato genome hasn't been fully sequenced/annotated which has proved problematic as my blast searches turn up a number of large sequences which I was prepared to believe were real homologues but also a number of small sequences which I'm not so sure about. I guess these could be parts of the larger sequences and so not a seperate result but the sequences don't match up perfectly so this makes it hard to judge whether any differences are sequencing errors or real.

I'm using BioEdit to align my sequences and I was hoping to use it to figure out which of my potato sequences is the homologue to the corresponding gene in Arabidopsis but I can't figure out a way to do it as its not obvious by eye. It doesn't help that the Arabidopsis genes are all pretty similar to each other as this makes it harder to find the corresponding one in potato.

Hopefully this makes sense, does anyone have any idea what tools I could use to discriminate between the sequences, aside from going through and counting nucleotide differences. I guess looking at the protein sequence could help?

Thanks very much

kumar.pranav 11-06-2010 09:14 PM

Re: issues with homologous genes and bioinformatics

You could check out Clustal-W. That's a tool to do multiple sequence alignment. You could align a whole family of genes from Arabidopsis( or just a few of them) with the potato sequence you have. You could very easily see the differences. There are a lot of discriminative options that can help you out.

But probably this is not what you are looking for, you need a tool that would score each of the sequences?

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