Question: Python bioinformatics mini project ideas
0
gravatar for Galaxy123
19 months ago by
Galaxy1230
Galaxy1230 wrote:

Hi,

As part of an assessment I have to write a short application in python that can perform task(s) relevant to Bioinformatics (e.g. converting between one DNA sequence format and another). If anybody has any ideas I would really appreciate hearing them.

Thanks!

ADD COMMENTlink modified 19 months ago by Bill Pearson860 • written 19 months ago by Galaxy1230

How short are we talking? You can do an amazing amount with a single line of code ;)

ADD REPLYlink written 19 months ago by Joe14k

It has to be between 100 and 500 lines of code

ADD REPLYlink written 19 months ago by Galaxy1230

I actually had an idea for a script I'd like to write myself earlier. I'd be interested the result if you wanted to take this on. I think this can easily be achieved within 500 lines of code (depending on how fully featured you make it). I don't know how difficult it'll be, but could be a fun one to write.

Here's how I would pose the challenge:

  • Given an arbitrary protein sequence, determine its lifetime inside the cell using the relationships defined in the "N-end rule"
  • Extend this to different cell types.

https://en.wikipedia.org/wiki/N-end_rule

ADD REPLYlink written 19 months ago by Joe14k
0
gravatar for Bill Pearson
19 months ago by
Bill Pearson860
Bill Pearson860 wrote:

Here is a project that requires you to look up refseq protein sequences at NCBI, find their Uniprot accessions, determine whether the NCBI and Uniprot proteins are in fact identical, and then asks whether the proteins contain complete Pfam domains:

https://fasta.bioch.virginia.edu/biol4230/labs/accessions_hwk5.html

ADD COMMENTlink written 19 months ago by Bill Pearson860
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