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Old 09-03-2012, 08:11 AM   #1
Darth Ghisus
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Default Nucleotide to amino acid translation + synonymous/non-synonymous count

Hi everybody,

I'm going to perform a SNP calling using SAMtools.
The source data consist of an invertebrate mitochondrial transcriptome and I would like to detect the synonymous and non-synonymous SNPs in order to perform some evolutionary tests, like Ka/Ks.
Basically, all I need is the number of synonymous and non-synonymous SNPs.

If no program is available, I could translate all the sequences and count those who match the reference amino acid sequence and those who don't. But I need a program to translate all my sequences from nucleotides to amino acid (using invertebrate mitochondrial code).
Suggestions?

Thanks a lot.

Fabrizio

P.S.: Softwares like Annovar are not useful to me, because I don't need a functional evaluation of my SNPs and, besides, I'm working on a non-model organism, so that kind of information is unavailable.

Cheers!!
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Old 09-03-2012, 11:42 PM   #2
TiborNagy
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I think SIFT is your program.
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Old 09-04-2012, 04:15 AM   #3
Balat
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you could also try 'popoolation'.
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invertebrate mitochondria, ka/ks, non-synonymous, synonymous, translation

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