Most efficient command line tool for translating the DNA sequences into Protein ?

Question

[sunnykevin97]

Hi,

What is the most efficient tool for translating the DNA sequences into protein? And remove the stop codons more robustly.

I tried TranslatorX, it detects a lot of stop codons, unable to translate some of the sequences which have termination codons.

The protein sequences I'll use for the phylogenetic studies.

Any suggestions.

[Mensur Dlakic]

For someone who has asked many questions on this forum, I don't think you are putting proper effort into making it clear what you want. What does it mean most efficient in this context? Fastest? And what does it mean to remove stop codons? Translation programs are meant to stop translating on stop codons. If you want something that will go through stop codons when translating, you need a promiscuous translator, not the most efficient translator.

If you spend more time formulating your questions properly, you are more likely to get a good answer, and also in a single iteration. Otherwise you will get lots of follow up questions to clarify - see above - and that is more work both for us and for you. In the end you will still have to do your part and explain properly, but might as well save us time needed to ask follow-up questions.

Answer 1

[brian.fristensky]

There is also pal2nal, from Suyama and colleagues. Pal2nal is part of the multiple alignment workflow in the BIRCH system, which includes elimination of duplicates using cd-hit, multiple alignment usind clustal omega or mafft, alignment of DNA to a protein alignment with pal2nal, and removal of gapped regions using Gblocks. See the BIRCH multiple alignmen tutorial at http://home.cc.umanitoba.ca/%7Epsgendb/tutorials/bioLegato/multalign/multalign.html.

[Mensur Dlakic]

Part of me doesn't blame you because the question is not clearly formulated, but really: How is this answering the central question (DNA translation into protein)?