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Old 02-08-2015, 03:31 AM   #1
Location: Canada, Quebec

Join Date: Apr 2012
Posts: 53
Default Is a bioinformatics tool to list mutations between two short bacterial sequences?


I have two bacterial sequences of 10 kbp in fasta format and I am looking for a bioinformatics tool which is able to list the mutations (Indels and point mutations) between both sequences.

I performed a global pairwise alignment of my sequences using needle (Needleman-Wunsch algorithm) from the Emboss package, which is known to produces an optimal alignment.

In a second time, I used MUMmer as indicated in the manual for snps/indels dectection:

However, there some differences (mainly for indels) between the alignment produced by needle (that I use as a quality control) and the result generated by MUMmer. I suspect that the differences come from the initial alignment produced by MUMmer.

Is there another tool (like MUMmer) for which I can give my own alignment?

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