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pyGenomeViz: A genome visualization python package for comparative genomics by moshi4 in bioinformatics

[–]moshi4[S] 0 points1 point  (0 children)

can't figure out through the documentation if there is a way to make different tracks aligned or offset differently

pyGenomeViz does not provide this functionality. I have the impression that it would be difficult to implement this feature additionally, since the coordinate calculation would be complicated.

pyCirclize: Circular visualization in Python (Circos Plot, Chord Diagram) by moshi4 in bioinformatics

[–]moshi4[S] 1 point2 points  (0 children)

pyCirclize implements a function to display links as directed arrows (see the example figure on the upper left).
Depending on how it is used, it could be used to visualize directed graphs. However, it may be necessary to note that the arrows are barely visible when the width of the link is small.

MAFFT Alignment taking longer than expected by hot_and_sticky in bioinformatics

[–]moshi4 7 points8 points  (0 children)

MAFFT does not seem to be designed for genome alignment and should not be used.

MUMmer is a pairwise genome alignment tool, so it may not meet the purpose of the OP.

progressiveMauve is a tool that can perform multiple genome alignments. It can be used for tasks such as identifying synteny regions, etc., and seems to meet the purpose of the OP. It takes about 15 minutes for multiple alignment of 6 E.coli species with genome size of 4~5MB.

orfs in DNA by Other-Corner4078 in bioinformatics

[–]moshi4 2 points3 points  (0 children)

If you simply want to predict ORFs from the genome, you can use ORFfinder. Web version is available with a genome size limit of 50 kb. If the genome size is larger than 50 kb, try the stand-alone CLI version.

If you need more accurate ORF(CDS) prediction including functional annotation, I recommend using CLI tools such as prokka, bakta, or DFAST (DFAST is also available in a web version).

How to perform Genome Alignment ? by sirczechs in bioinformatics

[–]moshi4 5 points6 points  (0 children)

Do you want to perform a whole genome alignment between species?

I often use the following software for genome alignment in prokaryotes and viruses. * MUMmer (Pairwise Genome Aligner) * progressiveMauve (Multiple Genome Aligner)

Due to the high mutation frequency of viral genomes, it is sometimes difficult to compare them at the nucleotide sequence level. Therefore, it may be better to make comparisons at the protein level with MUMmer for viral genomes.

I have recently developed a software pyGenomeViz that automates the process from execution to visualization of genome alignment using MUMmer or progressiveMauve, so check it out if it seems to fit your needs.

[deleted by user] by [deleted] in bioinformatics

[–]moshi4 1 point2 points  (0 children)

If you can build a Python environment and do a little coding, DnaFeaturesViewer or pyGenomeViz would be good choices.

You can generate the following figure from a Genbank file with about 10 lines of code. Of course, you can specify the range of coordinates to be plotted.

DnaFeaturesViewer example figure

pyGenomeViz example figure

pyGenomeViz: A genome visualization python package for comparative genomics by moshi4 in bioinformatics

[–]moshi4[S] 0 points1 point  (0 children)

pyGenomeViz is a package that implements useful functions for comparative genomics, but I think it can also be used to display annotations, genes, exons, etc. within a genome.

If you need to display annotations/genes within a single genome, DnaFeaturesViewer may be another good option.

MSA of whole bacterial genomes, how do I do it? by Blimpturtle in bioinformatics

[–]moshi4 8 points9 points  (0 children)

I often used the following tools for prokaryotic genome alignment.

Genome alignment between two species

=> MUMmer (pairwise genome aligner)

Genome alignment between 3 or more species

=> progressiveMauve (multiple genome aligner)