Skip to main content
3 votes
Accepted

Barrnap Bacterial rRNA Predictor script permission denied error when running Prokka

My suggestion is to run prokka from within conda by simply downloading miniconda then ...
M__'s user avatar
  • 12.5k
3 votes
Accepted

Problem installing RATT

Usually the home of a program is where the executable is. In order to make the system aware you need to include it as a variable when the terminal is run. So you need to add it to the file at ...
llrs's user avatar
  • 4,713
2 votes

Is there anything similar to GSEA for locus-based (instead of of gene-based) data?

I tinkered with a program GSEA-SNP quite a few years back, which claims that it does a similar ranking procedure with SNPs. It carries out its procedure by first linking SNPs with genes, then running ...
gringer's user avatar
  • 14.3k
2 votes

Find specific functional genes from a list?

BioMart. Filter by your list of genes and a GO term linked to acetyl transferase activity.
Emily_Ensembl's user avatar
2 votes

where to find pathogenicity metadata for E.coli genomes

you can use BacDive. This is the largest database for bacterial metadata.: https://bacdive.dsmz.de/ e.g. you can search for the sequence accession "NCTC8196" and you would get the metadata of the ...
user6331's user avatar
2 votes

How to parse hmmsearch output?

The TSV output should be sorted by default in a way that for a given query the top hit comes first, followed by other hits. For a quick extraction of top hits you may use a rather simplistic script: ...
darked89's user avatar
  • 358
1 vote

How to parse hmmsearch output?

Since we don't know what you are trying to maximize here, which of the various columns would define the "best" hit for what you are trying to do, here is a generic solution that will just ...
terdon's user avatar
  • 10.2k
1 vote

PANTHER FUNCTIONAL CLASSIFICATION in R

One approach is to get the gene's sequence (DNA/AA) and use the interproscan API (e.g., https://www.ebi.ac.uk/Tools/common/tools/help/index.html?tool=iprscan5) with the httr2 library in R to POST ...
Jacob Krol's user avatar
1 vote

I have a partially described gene from a plant, which tool may I use for predicting regolatory and UTRs sequences from a single DNA fragment?

Assuming that you know the gene name, you would be able to look it up in a transcriptome assembly presumably, or perhaps NCBI has a full length transcript (search ...
Maximilian Press's user avatar
1 vote

Bulk protein annotation with Prokka

Prokka doesn't need whole genomes, I've definitely used it for smaller contigs before so I think you're fine!
TW93's user avatar
  • 449
1 vote

Functional Annotation vs Functional Enrichment--which one should I use for Network Analysis?

The answer to your main doubt about "annotation vs. enrichment" is that you need both, but you already have one annotation. You can only perform a functional enrichment analysis after you ...
Lucio Queiroz's user avatar
1 vote

Differential Expression

I guess plasmodium doesn't have that many online tools dedicated to it so you can use the annotation packages from bioconductor and try it. I used clusterProfiler for analysis and org.Pf.plasmo.db for ...
StupidWolf's user avatar
  • 1,688
1 vote
Accepted

Why are my genes filtered for Gene Ontology term enrichment?

What is "click here for details" saying? That link should contain an explanation of what happened. GSEA usually requires entrez_id to run. If your list contains <...
fra's user avatar
  • 567
1 vote

Compare functional enrichment between genelists

To compare gene list based on gene ontologies you can use GOSemSim (Note, I'm a contributor to the package). You can select the semantic similarity to compare them, that is how the redundancies and ...
llrs's user avatar
  • 4,713
1 vote
Accepted

SnpEff gene annotation with @ such as PCDHB@

The @ at the end of a name denotes a "gene cluster in chromosome region". This is mentioned in the official HUGO nomenclature guidelines in the "Characters reserved ...
terdon's user avatar
  • 10.2k
1 vote
Accepted

RNA seq fasta file annotation from alignment to reference matches

An awk approach (assuming your input "csv" file is space-separated): ...
terdon's user avatar
  • 10.2k
1 vote
Accepted

Why does RATT create a directory with chromosome sequences and how can I stop it?

RATT seems to be a very simple wrapper script that unfortunately does not clean up its temporary files properly. Short of modifying the code yourself, your only option is to perform the cleanup ...
Konrad Rudolph's user avatar

Only top scored, non community-wiki answers of a minimum length are eligible