Hi there,

I'm having a bit of trouble trying to find out how to construct a particular pipeline using the Entrez E-utilities. Specifically, what I want to do is, do a search in the Taxonomy database, i.e.

Insecta[ORGN] AND genus[RANK]

Then, for each ID returned in that search, find all its IDs in the Nucleotide database, but then filter those Nucleotide IDs with a Nucleotide query, which is this:

cox1[gene]

Then get the FASTA sequences. And I would like to preserve the mapping between the IDs, so ideally I would get something like this:

tax_id_1 --> nucleotide_id_1 --> fasta sequence
tax_id_2 --> nucleotide_id_2 --> fasta sequence
...
tax_id_n --> nucleotide_id_n --> fasta sequence

(Where tax_id_1 and tax_id_2 are IDs from the Taxonomy query, nucleotide_id_1 is the COX1 gene sequence for tax_id_1, nucleotide_id_2 is the COX1 gene sequence for tax_id_2, etc.)

At the moment I'm using Python to do this, and then decided to do this through the browser (just to keep things simple). I have used Elink to handle the Taxonomy query, Elink to map from the Taxonomy IDs to the Nucleotide IDs (preserving the one-to-one correspondence), but I'm stuck on how to then filter those Nucleotide IDs so that I only get COX1 as the gene. I have tried doing this previously with varying degrees of success, and even if I did manage to pull it off, I'd probably have done it in such an unelegant way!

How would you go about doing something like this?

Cheers