EMBOSS transeq translate to protein with 3 letter code
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3.1 years ago

dear all,

would be possible to translate a nucleotide sequence with the three letter code using EMBOSS transeq? I can do it with the one letter code

$echo atgtttcaggacccacaggagtaa | transeq -filter -osformat2 text MFQDPQE*  But I don't see in the manual the 3 letter code. Thank you emboss transeq translation 3 letter code • 1.3k views ADD COMMENT 0 Entering edit mode If you don't see that option in the manual then no. You could do some replacements with sed if you must have three letter code. ADD REPLY 0 Entering edit mode Any particular reason why you want to do that? It will only be very confusing ... ADD REPLY 1 Entering edit mode Just for graphical reasons: with the three letter code, it is easier to see the correspondence with the triplette: atgttt... MetPhe...  ADD REPLY 1 Entering edit mode I find this even easier: atgttt M F  ADD REPLY 0 Entering edit mode yes but you need to add 5 spaces because the sequence is given as MF not ad _M__F_ ADD REPLY 1 Entering edit mode Not quite right, the general pattern is you have to insert one initial space, then two spaces between every amino acid, then a final space. There are several tricks around to split a string into characters. As I like perl, split //,$_ would split a string at every character, then join with join. The split PerlDoc has some examples of using them together.

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It wouldn't be too hard to write a script which converts between one and three letter codes. There must be ample python examples to get you started.

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sure, that is not the problem, just wanted to know if transeq does it directly to save the effort...

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3.1 years ago

The output peptide sequence is always in the standard one-letter IUPAC code.

http://structure.usc.edu/emboss/transeq.html

and try this:

\$ echo atgtttcaggacccacaggagtaa | showseq -filter -threeletter y -format 4

10        20
----:----|----:----|----
atgtttcaggacccacaggagtaa

MetPheGlnAspProGlnGlu***

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that is exactly what I have been looking for! thank you

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I have moved the comment of cpad0112 to an answer so it can be accepted.