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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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What is difference between gene and CDS in the gff file?

I'm investigating bacterial genome. In GFF file, it includes gene, CDS, tRNA or something like that in region fields. What is the difference between gene and CDS? Thant you in advance.
uri's user avatar
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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 ...
David's user avatar
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Approaches for filtering bacterial/fungal contaminant sequences from RADseq results

I'm working with RADseq data (288 compressed FASTQ files, *.fq.gz) from 3 plates of plant tissue. I've done demultiplexing and preliminary QC (using the Stacks <...
akoontz11's user avatar
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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 ...
K_081's user avatar
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1 answer
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Genetic relationships between Cyanobacteria: terrestrial vs aquatic

I believe one of the site members is an expert in Cyanobacteria hence the question. I'm looking for a comprehensive 'phylogenetic tree' of the phylum Cyanobacteria and want to identify all the ...
M__'s user avatar
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2 votes
2 answers
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What would be the best method to obtain every prokaryotic psychrophile genome?

I am interested in running an analysis on the genome of every psychrophilic bacteria. Here defined as bacteria that have an optimal growth temperature at less than 15°C. What would be the best way to ...
donkey's user avatar
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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 ...
M__'s user avatar
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3 votes
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Barrnap Bacterial rRNA Predictor script permission denied error when running Prokka

I am trying to run the Prokka annotation tool on my linux machine and have installed Barrnap and added it to $PATH and given the folder chmod 777 permission. However, when running Prokka, it gives the ...
Harish Prabhakar's user avatar
-2 votes
1 answer
137 views

How can I identify the virulence factors in my FASTQ files generated from nanopore sequencing bacteria DNA?

I have performed genomic sequencing using nanopore technology and upon analysing using BLAST in the command line I have identified the presence of E.coli. I was wondering if I can add some code to ...
wilkohollie's user avatar
1 vote
1 answer
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Is there a smaller representative version of refseq with fewer than 30K files in it?

Does any one have a condensed NCBI reference seq database with all the gbff files, which covers mostly all the bacteria and archaea. The current NCBI ReqSeq contains more than 30,000 gbff files. I am ...
flashton's user avatar
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1 answer
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Multivariate analysis of cell culture bioprocess

I am seeking statistical support for the following bacterial growth time series. In the lab, we have cell cultures growing in bioreactors. Every day we measure the concentration in mmol-1 of a set of ...
CorteZero's user avatar
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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 ...
Dev Desai's user avatar
2 votes
2 answers
178 views

Bacterial genomes and snpeff warnings 'WARNING_TRANSCRIPT_NO_START_CODON'

I annotated a bunch of genomes with snpeff. And although the original reads' qualities and the matches with the reference genomes were quite high, I see the above mentioned warning in almost every ...
Anti's user avatar
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1 answer
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Should I expect / use a prokaryote-specific substitution model when building a phylogenetic tree?

I have a couple of prokaryotic genes that I'm trying to build phylogenetic trees from. I inputted them into IQTree, which, as part of the workflow, runs through multiple substitution models until it ...
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2 answers
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How can I improve or otherwise investigate an unreliable genome tree?

Summary My genome tree doesn't agree with my gene trees and I get the feeling that my genome tree might be wrong, possibly due to long branch attraction, but I don't know how to check/fix it. ...
Laura's user avatar
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3 votes
4 answers
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How can I add a ";" at the end of each fasta header line in a file?

I have a large fasta file with RNA sequences. I need to add a ; at the end of each header line (lines beginning with >) in ...
Callahan McGovern's user avatar
2 votes
1 answer
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Questions about microbial 16s rRNA phylogenetic, ANI Taxonomy, and GGDC

I have a few questions about these three methods. We commonly use 16s rRNA to identify species and construct a phylogenetic tree. If there's a new isolate from a new and undiscovered ecosystem, ...
raysteven's user avatar
6 votes
2 answers
53 views

How to display novel genome assemblies or uncommon genome assemblies using the UCSC Genome Browser?

I want to display E.coli BW25113 (GenBank: CP009273.1) strain in UCSC browser. This strain is not listed in http://microbes.ucsc.edu/ browser. How can I display E.coli BW25113 assembly in the browser?
Supertech's user avatar
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-1 votes
1 answer
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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. ...
Negin's user avatar
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450 views

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 ...
HelpNeederStudent's user avatar
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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, ...
Mark's user avatar
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4 votes
1 answer
580 views

Bruker MALDI-TOF bacteria species identification scoring algorithm

Just wondering whether anyone can point me to a research paper which describes how the scoring values are generated by the Bruker software for species identification of bacteria in MALDI-TOF MS. For ...
There's user avatar
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4 votes
2 answers
76 views

What is the typical host-to-bug DNA ratio found in nanopore sequencing without amplification?

I'm interested in sequencing a human sputum sample using an ONT MinION without performing any type of whole genome DNA amplification or targeted PCR. Has anyone found a good reference (or anecdotal ...
TimD1's user avatar
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1 vote
2 answers
206 views

How can I get or create a reference genome for Bacteria?

I am a computer engineer and nowadays trying to grasp some concepts of Bioinformatics particularly, reference genomes and genomic variants. My aim is to find the effect of sequence features on variant ...
Tripoli's user avatar
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2 votes
1 answer
67 views

Populations genetics and dynamics of bacteria on a Graph

Disclaimer: I'm a physicist and I'm fairly new to Bioinformatics therefore somethings below may not make sense. My purpose: I would like to simulate genetic evolution of bacterial populations, ...
omega's user avatar
  • 123
2 votes
2 answers
130 views

How to fragment genomes into non-overlapping sequences of differing sizes?

I have bacterial chromosomes/plasmids that I have downloaded off refseq in a multi-fasta that I would like to fragment into non-overlapping fragments of between 1 kb and 15 kb. I have tried googling ...
Stanley Ho's user avatar
1 vote
2 answers
108 views

Bacterial DNA at the tail of transcriptome reads. What does that mean?

I am assembling a transcriptome obtained from the Internet. The transcriptome was extracted from a human cancer tissue that had been previously grafted into a mouse. I have detected that many ...
juanjo75es's user avatar
0 votes
1 answer
74 views

What is the origin of the 'source Gene ID' references given in the 'gene_presence_absence.csv' output of Roary?

I am learning to use Roary for preparing a pan genome for some lactobacillus strains. In the 'gene_presence_absence.csv' output of Roary (which I view in excel), a 'source Gene ID' is given for each ...
Mark's user avatar
  • 143
1 vote
1 answer
76 views

Visualizing cell growth

I model the following events: a rod-shaped cell with center $x$ grows symmetrically until it reaches a maximum length/age, it divides into two identical cells, and the process continues. At division, ...
a0142204's user avatar
2 votes
1 answer
125 views

How to construct the phylogenetic tree of the "High Recombination" genus streptomyces?

I need to construct the phylogenetic tree of the whole genus of streptomyces. And my goal is to find out how my target strep species distributed in the whole strep genus and obtain the distribution ...
TANGLi83's user avatar
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1 vote
2 answers
193 views

How many single copy gene are needed to construct the phylogenetic tree?

I ran the orthomcl program with genomes of the whole streptomyces genus(from ncbi) as input, but I only got 22 orthologous groups(streptomyces's genome size vary from 2M to 15M, which shows the great ...
TANGLi83's user avatar
  • 128
0 votes
2 answers
1k views

Looking for a tool to find 16S rRNA in hundreds of genomes

I have hundreds of bacterial genomes and I would like to know which is the best informatic tool in which I can run all genomes on one go and get a 16S rRNA gene sequence of each genome as output. ...
Manolo Dominguez Becerra's user avatar
2 votes
2 answers
111 views

Is there a "definitive" database for Mobile Genetic Elements?

This isn't quite my speciality, but I've been tasked with finding any evidence of Mobile Genetic Elements (like transposable elements, retrotransposons, bacteriophages, etc.) within some WGS samples. ...
EB2127's user avatar
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1 vote
3 answers
288 views

16S species-level taxonomic assignment--what is the current state of the art?

We currently use DADA2 for picking ASVs and the assignTaxonomy funciton for assingment to genera. Google does bring up various recent articles on species-level ...
abalter's user avatar
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1 vote
2 answers
2k views

Extract reads from bam files by their @RG

How could I extract reads from bam files by their read groups @RG ?, I've got one file containing all reads for 5 samples, the SM is appears NONE, So, I want to extract each sample reads by the @RG ...
Maloki's user avatar
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1 vote
1 answer
67 views

Annotating conserved protein domains in bacterial assemblies

I understand the basic principles under which RPS-BLAST operates: search a protein (rpsblast) or nucleotide (rpstblastn) query ...
Daniel Standage's user avatar
4 votes
1 answer
130 views

How to quantify similarity of genomes and find differences in set of S aureus genomes?

I have around 500 annotated proteomes of different bacterial strains and would like to quantify their similarity (or difference). I found gt genomediff from ...
Soerendip's user avatar
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1 vote
0 answers
39 views

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 ...
dedek's user avatar
  • 111
5 votes
1 answer
73 views

how do I predict bacterial small non-coding RNA for a specific mRNA?

I am working on Vibrio parahaemolyticus. I have a gene that it is possible might be regulated by small non-coding RNAs. How can I predict possible sRNAs that target the transcript of this gene. Most ...
Mohammad ALKADI's user avatar
5 votes
1 answer
130 views

CRISPR Sequence Finder and Database Download

I am searching for tools to pull CRISPR Spacers from Bacterial Genomes. I am aware of the CRISPRDB and the corresponding identification tool on the web server. Are there other tools for finding ...
Cody Glickman's user avatar
4 votes
2 answers
343 views

Gene function annotation - bacterial genome

I'm trying to annotate a genome to find all genes with a specific function. I have a FASTA and the read FASTQs - I'd like to assign the functional group of the identified proteins (e.g. Kegg orthology)...
MichaelKirst's user avatar