Determination of SNP's in genomic slands

Question

[arya]

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

[WouterDeCoster]

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

Answer 1

[arya]

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.

[WouterDeCoster]

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?

[arya]

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

[WouterDeCoster]

I think mummer could be a solution to this