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7 votes

How can I add a ";" at the end of each fasta header line in a file?

One way, using sed and a regex address to select only the header lines and apply a substitution to append a semicolon to the end of each line: ...
Steve's user avatar
  • 3,099
6 votes

How can I add a ";" at the end of each fasta header line in a file?

... using the legendary Perl pie perl -p -i -e 's/^(>.*)/$1;/' mybacteria.fa Input ...
M__'s user avatar
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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 ...
Bioathlete's user avatar
  • 2,574
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, ...
Harry Yoo's user avatar
  • 143
4 votes

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

... stuff of original post deleted. On second thoughts what you might be doing is a template assembly of your genomes. It is a possible interpretation of the 1.2. fasta sequences above (i.e. 1 is ...
M__'s user avatar
  • 12.3k
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 ...
Supertech's user avatar
  • 606
4 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 ...
M__'s user avatar
  • 12.3k
3 votes

How can I add a ";" at the end of each fasta header line in a file?

seqkit replace -p "$" -r ";" my.fasta > my.renamed.fasta Where -p is the pattern to match the end of ...
Ammar's user avatar
  • 143
3 votes

How can I add a ";" at the end of each fasta header line in a file?

I recommend to use Biopython as a clearer way. ...
Vovin's user avatar
  • 435
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. ...
M__'s user avatar
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3 votes
Accepted

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 ...
Alex Reynolds's user avatar
3 votes
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. ...
M__'s user avatar
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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
  • 12.3k
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://...
Cody Glickman's user avatar
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....
Geraldine_VdAuwera's user avatar
2 votes

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 ...
zorbax's user avatar
  • 769
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 ...
M.Bioinfo's user avatar
  • 374
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" ...
M__'s user avatar
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2 votes
Accepted

Bacterial genomes and snpeff warnings 'WARNING_TRANSCRIPT_NO_START_CODON'

Bacteria have a different translation table from eukaryote nuclear DNA; it may be that SnpEff is expecting human genes in the genome. Have you followed the build steps outlined in the documentation? ...
gringer's user avatar
  • 14.1k
2 votes

What would be the best method to obtain every prokaryotic psychrophile genome?

The database to use is BactoTraits. This will help either in the entirety or at least provide a solid starting point. Its here BactoTraits – A functional trait database to evaluate how natural and man-...
M__'s user avatar
  • 12.3k
2 votes
Accepted

What would be the best method to obtain every prokaryotic psychrophile genome?

I ended up copying the GenBank (primary) column from the REBASE search results into an excel sheet. From there, I created a file with one accession per line called ...
donkey's user avatar
  • 163
2 votes
Accepted

Genetic relationships between Cyanobacteria: terrestrial vs aquatic

Ah! Finally, a question I can answer. There has been some pretty good work about this recently. In particular, I would reccomend this paper by Chen et al. , which groups cyanobacteria into terrestrial ...
Laura's user avatar
  • 909
2 votes

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

CDS (Coding Domain Sequence) is just the protein - the sequence that is translated to amino acids. The gene for a bacterium should include the regulatory region, including the promoter and stop codon. ...
M__'s user avatar
  • 12.3k
1 vote

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

I am not sure if this qualifies as an official answer. I have contacted UCSC bioinformatics team. They were were very kind and told me that they would add any track that was requested by users. After ...
Supertech's user avatar
  • 606
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 ...
gringer's user avatar
  • 14.1k
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,...
There's user avatar
  • 151
1 vote

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

My recollection of a conversation I had with Justin O'Grady is that it's about 99% host DNA for unfiltered samples. There are a few ways to reduce that portion prior to sequencing. He has written a ...
gringer's user avatar
  • 14.1k
1 vote
Accepted

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

How can I get a reference sequence for other strains of E. coli? You can use any sequence you want as reference for a variation analysis. It just depends on the question you want to answer. So to ...
Mr_Z's user avatar
  • 629
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/...
swbarnes2's user avatar
  • 1,925

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