Is a bioinformatics tool to list mutations between two short bacterial sequences?

[Antony03]

Hello,

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: http://mummer.sourceforge.net/manual/#snpdetection

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?

Thank

[Brian Bushnell]

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.

Needleman-Wunsch does not yield optimal alignments. For optimality, under a model that assumes fewer mutation events are more likely than more mutation events, you need affine transforms to encourage insertions or deletions to be made adjacent rather than scattered around at random, which Needleman-Wunsch or Smith-Waterman will do because they are greedy algorithms.

That's just an aside, though. I don't know what tools would help you in this case.