[Baypiggies] upper case, lower case, and....?

Nick Stinemates nstinemates at gmail.com
Fri Apr 1 20:19:58 CEST 2011


My knowledge of chemistry is not very good, so please forgive my basic
questions:

Are protein sequences a pre-determined length?
Are the sequences in a way which can be parsed easily?

If so, you can basically create a parser for protein sequences, convert them
to some data structure which you can iterate through, and do whatever you
want with the sequences which contain a phospho serine character.

Does that make sense? With some of the rules in place, I can give guidance
on how to write it.

Nick

On Fri, Apr 1, 2011 at 5:13 PM, Dirk Bergstrom <dirk at otisbean.com> wrote:

> On 04/01/2011 06:01 AM, Vikram K wrote:
> > I have this protein sequence (each character represents an amino acid):
> >
> PEGKWLGRTARGSYGYIKttaveidydslkrKKNSLNAVPPRLVEDDQDVYDDVAEQDAPNSHGQSGSGGMFPPPPTDDEIYDGIEEEDDDDGSV
> > My problem is that i wish to distinguish the phospho serine character
> from
> > the rest of the small case letters in the modified protein sequence shown
> > above.
> > Any suggestions?
>
> *) Color
> Use ANSI escapes on the terminal, or css in html.  This is, IMNSHO, the
> rightest solution, as it gives you many degrees of freedom and is easy
> to see (as long as you don't end up with "angry fruit salad").  See:
>
> http://stackoverflow.com/questions/287871/print-in-terminal-with-colors-using-python
>
> *) Font weight
> Most terminals support bold via ANSI escapes.  If you're in html/print
> you've also got italics, underlined and strikeout.  Not as good as
> color, but usable in a B&W print article.
>
> *) Whitespace
> RGSYGYIK TTAVEIDYDsLKR KKNSLNAVPP
>
> *) Other characters
> RGSYGYIK|TTAVEIDYDsLKR|KKNSLNAVPP
>
> *) Depth
> On a 3D/holographic display, you can put the modified sequence above or
> below the rest of the protein.
>
> --
>        --------------------------------------
>       Dirk Bergstrom           dirk at otisbean.com
>              http://otisbean.com/
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