Extract start and stop codons in multiple seq alignment

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5.1 years ago

3335098459 ▴ 30

Hi,

I have multiple sequence alignment files and each contains around 450 sequences. I have been looking for software that extracts start and stop codon with sequence ID. Most of the questions in this and other websites were focused on deleting stop codons or extracting stop codon from one sequence. In EMBOSS, codon analysis table gives the total number of end codons that somewhat close to my query but I cannot get the specific sequence ID with stop codon.

Is there any possible way to find the solution?

Regards

Awan

sequence gene alignment • 1.4k views

ADD COMMENT • link updated 5.1 years ago by Pyretu ▴ 10 • written 5.1 years ago by 3335098459 ▴ 30

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Hey,

I do not know about a tool for such a "simple" task. Probably the easiest way would be to quickly write a script for this or use an awk/grep command to give you the lines of interest.

ADD REPLY • link 5.1 years ago by Pyretu ▴ 10

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How do you envisage this working if the alignment has split the codon? Did you do codon-aware alignment?

ADD REPLY • link 5.1 years ago by Joe 21k

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