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5 votes
Accepted

How to annotate a bacterial genome automatically?

There are a number of annotation pipelines that you could use to get fairly standardized annotation - Prokka has been around for a while (paper published in 2014) but is still used frequently. There's ...
KeyboardCat's user avatar
3 votes
Accepted

Dog (Canis lupus familiaris) MT gene annotations

Currently, there is no available mitochondrial sequence for the ROS_Cfam_1.0 assembly: https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_014441545.1/
Ben_Ensembl's user avatar
3 votes

Unable to install prokka using homebrew or conda

Prokka's github page github page has: conda install -c conda-forge -c bioconda -c defaults prokka edit Seems that there may be another way to do it: stepwise ...
darked89's user avatar
  • 368
2 votes
Accepted

Extract data from genome

This sounds like you are wanting to perform a machine learning calculation. However, for this question leveraging KEGG, Kyoto Encyclopaedia of Genome and Gene and building an SQL database around it is ...
M__'s user avatar
  • 12.6k
2 votes

Identifying the promoter on the reverse strand using visualization software (seqmonk)

Have a look at this UCSC browser shot. Looking at the WDR92 transcript, note that it is transcribed right to left. This would indicate that the promoter is on the right. Indeed, we see a variety of ...
Maximilian Press's user avatar
2 votes

What is the best Query to retrieve DNA from NCBI?

There are two main problems I can see in your approach. First, gene names are not standardized across species and the "same" gene (what that means is a whole different discussion) can have ...
terdon's user avatar
  • 10.2k
1 vote

Why is mtDNA not labelled as such for many organisms?

The most obvious answer is wet-lab rather than bioinformatics: mtDNA can get removed in the DNA extraction process. As a control group, in bacterial drug-resistance studies the plasmids are frequently ...
M__'s user avatar
  • 12.6k
1 vote
Accepted

What is the best Query to retrieve DNA from NCBI?

The search term you need is [gene name] rather than [title]. For example, ...
M__'s user avatar
  • 12.6k
1 vote

Annotation result for phylogenetic analysis shows no common evolutionary gene in contigs, can i change the contigs?

ITS: what is needed is the aim of the phylogenetic investigation. ITS evolves very quickly so it's good for a few closely related species and sub-species. Understanding the behaviour of a locus is as ...
M__'s user avatar
  • 12.6k
1 vote

How to interpret a GenomeScope plot?

Based on the numbers shown above the plot, and the appearance of the curve, this looks like reads from a diploid genome approximately 113Mb in length that was sequenced at around 174X coverage.
gringer's user avatar
  • 14.3k
1 vote

Why is there gene without annotated location?

This gene/protein appears to have been described exclusively as an isozyme / electrophoretic mobility assay of a protein. See for example this PepC mutant page: The Pepc locus controls ...
Maximilian Press's user avatar
1 vote

Extract data from genome

I've used Augustus stand alone (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1160219/) to find genes in a given eukaryotic genome. I agree you can then use things like KofamSCAN to categorize the ...
Rainman's user avatar
  • 171
1 vote

Finding annotated counterpart after BLASTn with efetch (Biopython)

Lets assume you can get the blastn output in a BED format: ...
darked89's user avatar
  • 368
1 vote

Finding annotated counterpart after BLASTn with efetch (Biopython)

It seems like the seq_start and seq_end are sensitive to the direction. Try swapping the two.
RaphiS's user avatar
  • 11

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