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Determination of SNP's in genomic slands

Hi I am trying to determine SNP's between a genomic island found in different genomes. The island sequence is about 50kb. Pls suggest me a tool that will help me in the same. Thank you

snp snp next-gen genomic islands
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written by arya • arya

Did I understood correctly that you are looking for paralogous sequence variants between multiple copies of a repetitive sequence in multiple reference genomes?

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written by WouterDeCoster WouterDeCoster

1 answer

Thanks for showing interest in my query. To make my post more clear, I have about 25 genome sequences in hand which contain a particular island sequence. I have retrieved the island sequences from each and wish to compare them with an already reported complete sequence of the same island (which would be like a reference) and determine the SNP's (if any). I hope I have clarified.

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written by arya • arya

Please use ADD COMMENT or ADD REPLY to answer to earlier comments, and such this thread remains logically structured and easy to follow.

So your data is in fasta format and you want to find pairwise differences with a reference fasta?

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written by WouterDeCoster WouterDeCoster

Thanks for your suggestion. Coming to your question Yes, I have them in fasta format.

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written by arya • arya

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