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7 votes
1 answer

ANY (technical) reason behind submitting sequences to GenBank versus ENA Sequence

The DNA sequence sections of the three INSDC databases (i.e., DDBJ, ENA Sequence and GenBank) are synchronized periodically and strive to keep their stored data as ubiquitously accessible as possible. ...
Michael Gruenstaeudl's user avatar
3 votes
1 answer

How to get the uniparc ids for all members of uniref cluster in batch request?

I currently use the 'UniProt website REST API' (example) to collect the UniParc IDs of all the members of the given cluster. Fetching each entry individually is very slow though, so I wanted to ask if ...
C. Zeil's user avatar
  • 121
2 votes
2 answers

Error with eggNOG-mapper jobs

I recently tried using eggNOG-mapper for pan-genome and core genome analysis of files from OrthoFinder, specifically the 'Orthogroup_Sequences' which contains a huge list of protein files in fasta ...
K_081's user avatar
  • 149
2 votes
1 answer

Search ChebiEntity search by common or synonym name?

I can download information from ChEBI if I know the corresponding ChEBI ID: from libchebipy import ChebiEntity chebi_entity = ChebiEntity("15903") And ...
Soerendip's user avatar
  • 1,295
2 votes
0 answers

RATT works on example bacterial sequence and other bacterial genome but not on C. elegans genome and annotation

I am trying to use a tool called RATT described in this paper and available here. I ran the example using the following command: ...
Biomagician's user avatar
  • 2,459