Sequencing analysis for detection of mutations - (Mar/30/2011 )
I would like to ask is there any free software which can utilize sequencing file from 3130 sequencer, for detection of mutation. It would be better if it can mark the SNP and mutation automatically.
I've met software that can do that, but that was everything but not free. Pretty expensive.
But it's not that difficult to use a sequence viewer like FinchTV (my favourite, requires registration to download for free) or Chromas Lite, check the sequence visually for heterozygous mutations (you'll see two peaks in one spot), BLAST the sequence (FinchTV has a right-click option to directly BLAST selected sequence) to see sequence coverage and identity.
If you find a mutation, you can localise it on a corresponding gene in the Ensembl database, that shows nucleotide and protein sequence underneath in the cDNA view.
If its just Mutation detection, I would recommend Mutation Surveyor.
Download is free, get some trial period (30 or 60 days) after which, it does not allow you to export reports or something. But the best part, is that it calls on mutations and looks them up and reports them directly.
So, it will call a previously reported mutation directly by its name. something like G308A in TNF alpha.
edit: does NOT allow.