User: Richard Llewellyn
Richard Llewellyn • 170
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Computational biologist working on protein function inference methods via comparative genomics, especially genome context methods.
Posts by Richard Llewellyn
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... Hey,
I can't get UniProts programmatic mapping to only return the requested identifier any more -- rather it returns a list of many associated fields.
My python code from a year or so ago isn't working to map identifiers via UniProts REST service (https://www.uniprot.org/help/api_idmapping). I ha ...
written 5 months ago by
Richard Llewellyn • 170
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... Thanks for your perspective.
For those of us interested in a complete as possible picture of prokaryotic protein space, I think we now have to move to Uniparc as the primary reference. It might not be your case, but a significant number of the proteins made 'redundant' actually have no clear homol ...
written 3.7 years ago by
Richard Llewellyn • 170
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... My work involves comparing similar prokaryotic organisms, and since Uniprot reduced their coverage by determining many proteomes 'redundant,' I can no longer rely on Uniref90 or Uniref50 to aid in clustering proteins based on sequence similarity. Apparently Uniref uses Uniprot, not Uniparc, as its ...
written 3.7 years ago by
Richard Llewellyn • 170
• updated
3.7 years ago by
dankwc2000 • 20
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... I haven't given up on using the GENOME_REPORTS prokaryotes.txt file, but there is an added wrinkle -- the bioproject_ids are 'GenBank' ids, while the genomes in the ftp "Bacteria" are 'RefSeq' bioproject_ids, so I'll need to cross-ref using ftp://ftp.ncbi.nlm.nih.gov/bioproject/refseq-genbank.csv.
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written 5.3 years ago by
Richard Llewellyn • 170
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... Thanks. I've used them in the past, but need to be more current (want to have at least 95% of completed genomes already deposited in NCBI). I'll check there again though.
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written 5.3 years ago by
Richard Llewellyn • 170
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... Yeah, similar history here. One kludge after another. I find it disheartening that NCBI has given up on subspecies taxids, as there is no controlled vocabulary for these.
I could toss files, but my goal is to parse all available prok genomes, and that Vibrio example may be a harbinger of what is ...
written 5.3 years ago by
Richard Llewellyn • 170
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... Nope, that's what I had hoped (and then it would be simple), but folders sometimes contain multiple strains, or even multiple unrelated organisms, such as:
ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Vibrio_parahaemolyticus_O1_K33_CDC_K4557_uid212977
and yes, in the example it is easy enough to read t ...
written 5.3 years ago by
Richard Llewellyn • 170
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... That file looks promising (+1 for the reminder and showing the headers). I'll parse it and see if it is complete and accurate enough to list all the molecules in the *.gbk files unequivocally with their source organisms.
...
written 5.3 years ago by
Richard Llewellyn • 170
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... Thanks for that thought -- I agree the /plasmid tag can be useful.. By an organism's genome, I mean all the DNA carried by an organism, plasmids, chromosomes, and prophages, so I want to match all of these gbk files to the organism (host if you prefer) from which they were sequenced.
Separately, I ...
written 5.3 years ago by
Richard Llewellyn • 170
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... Now that NCBI has given up assigning sub species level taxonomy ids (taxids), I am revisiting our method of building genomes from the *.gbk files at ftp.ncbi.nih.gov/genomes/Bacteria. In the past I hoped that taxids would eventually allow exact matching of sequence to the source organism, but this ...
written 5.3 years ago by
Richard Llewellyn • 170
• updated
3.3 years ago by
Biostar ♦♦ 20
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