[EMBOSS] protein three-to-one and one-to-three

[Peter Rice]

Dear Daniel,

On 25/09/2012 12:48, Rozenbaum, Daniel (Biocceleration Inc) wrote:> Hi,
 >
 > Our users are interested in having access to "three-to-one" and 
"one-to-thee" amino acid representation conversion utilities similar to 
these:
 >
 > http://bioinformatics.org/sms2/three_to_one.html
 > http://bioinformatics.org/sms2/one_to_three.html
 >
 >From what I've been able to tell, the latter is achievable with 
"showpep -three" (even though the users would have preferred a 
horizontal representation of the three-letter codes), and the only 
relevant library function currently available in EMBOSS is the 
embPropCharToThree() ; is this correct? those

Much discussed in the early days when we decided to offer 3-to-1 for
who found the letters hard to read but not the reverse direction because 
a 3-letter protein sequence can also be a valid 3x longer 1-letter 
protein sequence.

 > Just wanted to make sure that I'm not missing anything if we decided
 > to take a shot at developing such utilities within the EMBOSS
 > framework.

Easy enough to develop, but I would suggest using some output format 
that makes it clear it is not a standard sequence format - otherwise 
EMBOSS (e.g. seqret) will try  to read it as some other format and claim 
success. If your 3-letter output is unreadable then you can safely try 
implementing it as an input format.

regards,

Peter Rice