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Questions tagged [bacteria]

One of the three domains of life, with Archaea and eukaryotes. Bacteria, along with Archaea, are prokaryotes, i.e. lack a nucleus.

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How to use HGTECTOR tool for identifying HGT genes in a bacterial genome?

I wanted to know the HGT genes in a Metabacillus strain and I noticed that several papers use HGTector for this purpose. I installed HGTector through conda and tried to download the database for ...
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eggNOG API, how's it work?

Background eggNOG uses seed orthologues which correspond to its own internal database, so for example J421_1876 can be placed in its online search engine here. This ...
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Compare illumina sequencing output with reference genome

I am new to whole genome sequencing. I want to compare illumina whole genome sequencing of mutants of a particular bacteria with a genome (not annotated) of the original strain to look for what the ...
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How to modify dot plot in MUMmer 3 for bacteria comparative genomics?

I was trying to make a dotplot to visualize genome-genome sequence alignment by using the MUMmer 3 software (it is typically used to compare whole genome sequences of bacteria). I runned the same ...
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Why is Clostridium difficile toxin A + B outdated in snomed?

I'm looking at the new version of the Snomed dictionary and the concept 707993000 Clostridium difficile toxin A + B (substance) is deactivated (and outdated) since ...
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Aside from the header info, is there any way to distinguish between sequences generated by MiSeq and MiniSeq platforms?

I am comparing Illumina MiSeq (using MiSeq v3 kit) and MiniSeq (MiniSeq High Output kit) instruments for sequencing E.coli and Salmonella. I am curious if there is any way to bioinformatically ...
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Search for specific sequence in group of bacterial genomes

I have a group of L. plantarum genomes. I identified the pangenome using Roary. From the pangenome, I was able to identify unique 'genes' for some of the strains. One of these (actually several were, ...
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Evolutionary speaking, what are the constraints on having new mutations?

Evolutionary speaking, some mutations lead to better fitness of an organism and its adaptation to the environment changes, but I was wondering if there are some constraints on having new mutations. ...
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