Python bioinformatics mini project ideas

Question

[Galaxy123]

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!

[Joe]

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

[Galaxy123]

It has to be between 100 and 500 lines of code

[Joe]

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

Answer 1

[Bill Pearson]

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