[Biopython] [GSoC] Please submit your GSoC 2018 project ideas until Jan 20th.

João Rodrigues j.p.g.l.m.rodrigues at gmail.com
Wed Jan 17 10:47:25 UTC 2018

Also, an idea that I had in mind for a while is to add some sequence
analysis functionality, coupled to the Alignment class. For instance, I've
worked with alignments that I needed redundancy removed from, or
column-specific analysis like conservation, variability, coverage (# of
gaps), etc. I wrote some functions here and there but maybe there are
others with the same need that would like to see this implemented? I
thought also we could integrate this with Bio.Graphics and have some
graphical representation of alignments too, for these properties we would
calculate. Just putting out there for others to comment/criticize.

2018-01-17 12:44 GMT+02:00 João Rodrigues <j.p.g.l.m.rodrigues at gmail.com>:

> Hi Sourav,
> I'd keep the discussion on the list so others can give some input too :)
> Ah, secondary structures, I was thinking about tertiary! What kind of
> analysis would you have in mind? Do you have a paper (or your own example)
> or so where people do analysis you would like to add? Adding to this, would
> it be interesting to combine this with 3D structures of RNA, to for
> example, compare predicted secondary structures with 3D models?
> Cheers,
> João
> 2018-01-17 12:34 GMT+02:00 Sourav Singh <ssouravsingh12 at gmail.com>:
>> Hello,
>> I was thinking along the lines of integrating ViennaRNA's RNAfold or
>> other similar modules into Biopython for the parsing and analysis of
>> secondary structure of RNA's- Dot-bracket, Extended Dot-Bracket, WUSS
>> format. I am not sure if this is already available as a feature in
>> Biopython but I believe this should be a good feature to add if it is not
>> available.
>> Regards,
>> Sourav
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