46197 - پروژه بیوانفورماتیک (کولب / پایتون / الفافولد / پایگاههای داده بیوانفورماتیکی).

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پروژه بیوانفورماتیک داشتم  با پایتون

رشته : بیوانفورماتیک 

نرم افزار : کولب ، پایتون ، الفافولد و پایگاههای داده بیوانفورماتیکی 

پروژه درسی هست

Task 1 - 

* Download the UniProtKB proteins for C. albicans

* Download the FungiDB proteins (latest release) for C. albicans SC5314 and a table mapping from FungiDB to UniProt identifiers, e.g. using a FungiDB search: https://fungidb.org/fungidb/app/search/transcript/GenesByTaxon and then customising a tab-separated download (you will need to register for a free account).

* Using data available in FungiDB (which stores mappings from FungiDB genes/proteins to UniProt), or using any sequence similarity method of your choice, establish how many proteins are identical between the two databases

* Find proteins that are present in FungiDB but absent in UniProt, and generate one or two simple tables or charts to summarise the counts and identities of these genes/proteins. You may wish to explore if there is anything unusual about these in terms of their protein length, count of exons, or functional annotations compared to those that are identical between databases.

Task 2 – 

* Download the AlphaFold2 predictions for Candida albicans from the AF2 database. These have been generated from UniProtKB sequences for C. albicans.

* Extract pLDDT scores for each protein from the zipped pdb files for each protein. In the example below, the pLDDT scores are 35.61, 36.91… For each protein, calculate the mean pLDDT and the count of residues with pLDDT > 80.

* Create a histogram of these scores for the C. albicans proteome

From the output from Task 1, find a handful of proteins (say 5-10) present in FungiDB but without a clear mapping to a UniProt protein. For these, generate AlphaFold models for them, e.g. using ColabFold in the browser.

Generate scores as above for these structures. How do they relate to the profile of the whole proteome, do you think there is evidence that these are “real proteins” or perhaps incorrect gene model annotations?

For any that you think are plausibly real proteins, try some FoldSeek searches with them, and see if you can assign a function – write a few sentences to explain your findings.

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