Re^3: Debugging Bioperl warnings for Genebank files that are missing info

If you find an easier way to get the CDS and the protein sequences please let me know. Even if it involves not using Genbank, as long as I can use NCBI's FTP everything is fine...

"not using Genbank" and "as long as I can use NCBI's FTP" seems a bit contradictory. GenBank is NCBI, no?

Perhaps UniProt.org has what you want? (You haven't said what it is that you're after...)

For example, 742726 being your tax_id (taxonomy ID), it delivers the proteins with http://www.uniprot.org/uniprot/?query=taxonomy:742726&sort=score

I see there is a gff tab for download (easily turned into a URL).

As far as I know, NCBI, Ensembl, and UniProt exchange sequences and annotation regularly.

Comment on Re^3: Debugging Bioperl warnings for Genebank files that are missing info

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Re^4: Debugging Bioperl warnings for Genebank files that are missing info by Sosi (Sexton) on Oct 27, 2014 at 10:30 UTC
Eh indeed that is contradictory. I guess, in my mind I was thinking "well, I don't mind using some other approach, as long as I can use NCBI so that all info retrieved is consistent". Now, given the problems that I've found, I guess "consistency" is not the best word to describe NCBI's FTP.. The idea of using Uniprot is ok for retrieving the proteins. I am now trying to see if there is an easy way to retrieve their genomic sequences because this is the big problem that I am facing now. Also, I added a snippet of the kind of output that I would like to get.	[reply]

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Re^4: Debugging Bioperl warnings for Genebank files that are missing info
by Sosi (Sexton) on Oct 27, 2014 at 10:30 UTC

Eh indeed that is contradictory. I guess, in my mind I was thinking "well, I don't mind using some other approach, as long as I can use NCBI so that all info retrieved is consistent". Now, given the problems that I've found, I guess "consistency" is not the best word to describe NCBI's FTP..

The idea of using Uniprot is ok for retrieving the proteins. I am now trying to see if there is an easy way to retrieve their genomic sequences because this is the big problem that I am facing now.

Also, I added a snippet of the kind of output that I would like to get.

[reply]