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
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