4 votes

Gene function annotation - bacterial genome

The PATRICBrc.org is a free resource you can annotate your genome and compare it with publicly available genomes. Refer this tutorial for more detail. Once you have annotated your genome in PATRIC, ...
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  • 143
4 votes

Extract reads from bam files by their @RG

Typically I use samtools for operations like this. Specifically I use samtools view with either -r or ...
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  • 2,556
4 votes

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

I found two methods: You want to visit this page for instructions for novel assemblies: http://genomewiki.ucsc.edu/index.php/Assembly_Hubs . However, before doing that I highly recommend that you ...
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  • 326
3 votes
Accepted

Populations genetics and dynamics of bacteria on a Graph

I assume you are simulating a null distribution. Are you investigation recombination?? My main advice is to use population genetic terminology rather than geomometry to describe your simulation (e.g. ...
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  • 7,339
3 votes
Accepted

Questions about microbial 16s rRNA phylogenetic, ANI Taxonomy, and GGDC

I do understand that you are working with is an isolate and thus what occurs in metagenomics you feel is over doing it, particularly if 16S is e.g. >99% similarity via Blast. Before reading ...
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  • 7,339
3 votes
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How to fragment genomes into non-overlapping sequences of differing sizes?

You could use numpy.random.randint to sample integers from a uniform distribution, from 1000 to 15000 nt, extracting subsequences of that length from a linearized ...
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2 votes

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

Answer from @llrs, converted from comment: You could try to download RNAseq data from this bacteria and see if some of the RNA align to your sequence. You could try to blast your gene and look for the ...
2 votes
Accepted

CRISPR Sequence Finder and Database Download

CRT (CRISPR Recognition Tool) http://www.room220.com/crt/ Crisprs Finder Online Tool https://crispr.i2bc.paris-saclay.fr/Server/ Piler-CR http://www.drive5.com/pilercr/ (Omic Tools List) https://...
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2 votes

Extract reads from bam files by their @RG

This sounds more like a job for samtools split if you want to split out all the read groups into separate bams in one go. http://www.htslib.org/doc/samtools-split....
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2 votes

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

Would advise doing Denovo identification method structure-based. Then use these public databases ( RepBase, Dfam ) to look for high similarity or homology exploration, this possibility if your ...
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  • 364
2 votes
Accepted

How can I improve or otherwise investigate an unreliable genome tree?

The difficulty in answering the question is: The absence of "Y" in the "Gene of interest" tree The sampling bias in the number of taxa mostly between the "genome tree" ...
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  • 7,339
1 vote
Accepted

Should I expect / use a prokaryote-specific substitution model when building a phylogenetic tree?

IQTree is a fashionable method for speeding up bootstrapping and used on ultra large datasets. What IQTree might be doing is rigidly fixing a model and parameterisation is not estimate via the ML. ...
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  • 7,339
1 vote

Bruker MALDI-TOF bacteria species identification scoring algorithm

For identification scoring, the software correlates signal intensities of matched signals of mass spectra. The three scores obtained from such a procedure are multiplied and normalized to a value of 1,...
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  • 141
1 vote

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

I've previously written my own script to fragment DNA sequences (input as either fastq or fasta files) into identical-length fragments, with a given overlap. I used this because there was a particular ...
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  • 11.7k
1 vote

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

What exactly is the sequence? Are you sure it's not an artifact of the library prep? 5 seconds of googling turns up this: https://support.illumina.com/content/dam/illumina-support/documents/...
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  • 1,662
1 vote

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

From time to time these situations are encountered, notably when PCR is being deployed in rare DNA samples. In this instance the wiki states, Ralstonia solanacearum is an aerobic non-spore-forming, ...
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  • 7,339
1 vote

Visualizing cell growth

I would recommend looking into Python's plotting utilities, for example here. I would recommend specifically looking at the examples that plot mathematical functions. The basic idea is that you ...
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1 vote

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

You need bootstrap support using a model-based tree building algorhithm, via maximum likelihood (a few people use Bayes). The file format is relaxed phylip format (please submit a separate question if ...
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  • 7,339
1 vote

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

I would say, 120 markers is enough for phylogenetic analysis. see https://gtdb.ecogenomic.org/
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  • 196
1 vote

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

The one thing that strikes me is that OrthoMCL was written under David Roos supervision, which really means it was written with Toxoplasma gondii in mind, i.e. a eukaryotic parasite with notable ...
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  • 7,339
1 vote

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

You can use Barrnap barrnap -k bac --threads "$(nproc)" \ -o output_rrna.fna < input_file.fna \ > output_rrna.gff 2> /dev/null Put the ...
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  • 724
1 vote

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

Back in the Day™ RepeatMasker[1] was the go-to tool everyone used for TE annotation in eukaryotes. At the time, the RepBase database from GIRI[2] (license required) was the de facto database ...
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1 vote

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

I have been using dada2 and phyloseq (phangorn for trees) combination to analyze a V4 region 16s rRNA data set. I find their approach and explanations very understandable and usable since I prefer R. ...
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1 vote

Annotating conserved protein domains in bacterial assemblies

The first option. Using a pre-existing tool, such as PROKKA etc. Diversity. Bacterial diversity is staggering and species such as E. coli and Salmonella, which are closely related diverged when ...
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  • 3,529
1 vote

Gene function annotation - bacterial genome

Im not 100% on what you are looking for - you seem to jump from annotation to detection of genes in your question. But if you have a database of genes you want to detect (presence/ absence) you ...
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  • 925

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