I am enriching RNA-seq data for the fungus Neurospora crassa and would like to be able to search the genome by functional category, determine similarity of genes by category membership, and any other information I find interesting in Python or R. There are many websites that have this information, but the most comprehensive appears to be Pedant.

I would like to download a SQL database, a JSON file, or even a text file that contains the information on these sites without having to use a web interface for everything.

The data I need access to is gene code, gene description, DNA sequence, FunCat category, GO category, and maybe others on the Pedant site. Is there anyway to to programmatically access these fields or download all of them in bulk?

Note: I have been using the python bioservices module, but it only gives access to KEGG, which is missing information on many of the genes in the N. Crassa genome.

  • $\begingroup$ Did you try biomart? I don't think it retrieves FunCat information though. But you can get everything else. It has a python API as well as an R interface (in bioconductor). BTW what do you mean by gene code? $\endgroup$ – WYSIWYG Dec 25 '14 at 9:05
  • $\begingroup$ By gene code I meant locus number (NCU#####). I will look into biomart to see if it has the pathway information I need. $\endgroup$ – caburke Dec 29 '14 at 2:42

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