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This is a follow up to my early issue (#58) with some more data. Note that I'm not sure if the issue is in vcfanno or in vcf2db.
Sometimes, vcfanno would leave a record empty, for example (referenc…
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We need some guidance for some phage terms for PMID:28813669 and PMID:22726436.
1. In the paper it describes a phage encoded protein shell (which they call the "phage nucleus") that contains DNA an…
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For instance in PDB 4jjk, for ligand molecule FOL. If I use selection string: `:A and polymer`, the FOL molecule is included in the selection, when it shouldn't because it is not part of the protein c…
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From @thomaspd's email:
> Hi all,
>
> A change in the GAF format is coming, probably in July. The only change will be the qualifier column. For BP annotations, there will be additional qualifiers…
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#### Current behavior:
15 genes are discovered to be uncorrelated with their corresponding reactions in `Glycerolipid metabolism`/`Glycerophospholipid metabolism`/`Fatty acid oxidation`.
|…
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Hello,
I am trying to annotate a file of protein calls (i.e., a Prodigal metagenome output file) using microbeannotator. My file is 750M with 2,000,000 reads and an average sequence length of 275 …
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The following is the list of signal or transit peptides given as EWASes in Reactome:
1-58 of O00116 is a transit peptide (Reactome:R-HSA-9033519)
1-26 of P09110 is a transit peptide (Reactome:R-HS…
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``` sparql
PREFIX uniprotkb:
PREFIX rdf:
PREFIX faldo:
PREFIX up:
PREFIX taxon:
PREFIX skos:
SELECT ?MainGeneName ?SwissProtAC ?FTId ?aa_change ?type ?dbsnp ?disease
WHERE
{
?SwissProtAC…
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Hi,
I have just run into `Error: Incomplete database file. Database building did not complete successfully`. I used the following file as protein evidence:
[NbenthamianaGenbankAA.clean.fasta.gz](…
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Hi,
I am using Chromosembler to produce pseudochromosomes by mapping my scaffolds to the chromosome-level reference of a closely related species. An issue I'm facing is that after producing pseudoc…