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Alignment CDS with AA

Alignement Software

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4 replies to this topic

#1 ostiaziocan

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Posted 09 April 2013 - 08:47 AM

Hello!

Does anybody know any software to align a CDS with the its translated AA sequence with position number on both? When I do site specific mutagenesis I know the target aminoacid number and I would like to know immediately the codon to be mutated.

Thanks a lot

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#2 bob1

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Excellent

Posted 09 April 2013 - 12:38 PM

Most DNA analysis software will do this easily. I use ApE (A plasmid Editor, freeware) which has this function.

#3 ostiaziocan

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Posted 11 April 2013 - 08:00 AM

Thanks for fast reply! Nice software :) In the lab. we have Geneious. Ii does show the codon that correspond to an aminoacid but it does not tell you the position of the aminoacid. Not very useful if you only know the aminoacid position to mutate (i.e. S1848, T333...etc) and want to figure out the codon....

Thanks again

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#4 bob1

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Posted 11 April 2013 - 12:19 PM

Ah, I see, I'm not sure that ApE does this then. It does do an alignment with the position in the sequence you are using and the translation with a * every 5 bp and a few other things using the Text map function (enzmyes>textmap).

#5 ostiaziocan

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Posted 11 April 2013 - 02:34 PM

Thanks,
Yes, I think it does. The software shows the aminoacid position and when you select it, the correspondent codon is highlighted in the CDS.

Best





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