Nucleotide to amino acid translation + synonymous/non-synonymous count

Darth Ghisus · 09-03-2012, 08:11 AM

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!!

TiborNagy · 09-03-2012, 11:42 PM

I think SIFT is your program.

Balat · 09-04-2012, 04:15 AM

you could also try 'popoolation'.

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09-03-2012, 08:11 AM	#1
Darth Ghisus Junior Member Location: Los Angeles Join Date: Sep 2009 Posts: 1	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!!

09-03-2012, 11:42 PM	#2
TiborNagy Senior Member Location: Budapest Join Date: Mar 2010 Posts: 329	I think SIFT is your program.

09-04-2012, 04:15 AM	#3
Balat Member Location: Australia Join Date: May 2010 Posts: 36	you could also try 'popoolation'.