BOL: Related items

DnaSP: DNA Sequence Polymorphism, is a software package for the analysis of DNA polymorphisms

Neel — Wed, 25 Nov 2020 19:51:38 -0600

DnaSP, DNA Sequence Polymorphism, is a software package for the analysis of DNA polymorphisms using data from a single locus (a multiple sequence aligned -MSA data), or from several loci (a Multiple-MSA data, such as formats generated by some assembler RAD-seq software). DnaSP can estimate several measures of DNA sequence variation within and between populations in noncoding, synonymous or nonsynonymous sites, or in various sorts of codon positions), as well as linkage disequilibrium, recombination, gene flow and gene conversion parameters.

Address of the bookmark: http://www.ub.edu/dnasp/

FGENESH - Program for predicting multiple genes in genomic DNA sequences

BioStar — Thu, 20 Dec 2018 11:55:08 -0600

FGENESH is the fastest (50-100 times faster than GenScan) and most accurate gene finder available - see the figure and the table below. In recent rice genome sequencing projects, it was cited "the most successful (gene finding) program (Yu et al. (2002) Science 296:79) and was used to produce 87% of all high-evidence predicted genes (Goff et al. (2002) Science 296:79).

Address of the bookmark: http://www.softberry.com/berry.phtml?topic=fgenesh&group=help&subgroup=gfind

GeneOverlap: An R package to test and visualize gene overlaps

Jit — Thu, 27 Dec 2018 19:45:52 -0600

Overlapping gene lists can reveal biological meanings and may lead to novel hypotheses. For example, histone modification is an important cellular mechanism that can pack and re-pack chromatin. By making the chromatin structure more dense or loose, the gene expression can be turned on or off. Tri-methylation on lysine 4 of histone H3 (H3K4me3) is associated with gene activation and its genome-wide enrichment can be mapped by using ChIP-seq experiments. Because of its activating role, if we overlap the genes that are bound by H3K4me3 with the genes that are highly expressed, we should expect a positive association. Similary, we can perform such kind of overlapping between the gene lists of different histone modifications with that of various expression groups and establish each histone modification’s role in gene regulation.

Address of the bookmark: https://bioconductor.org/packages/release/bioc/vignettes/GeneOverlap/inst/doc/GeneOverlap.pdf

Termal: a fast and interactive terminal-based viewer for multiple sequence alignments

LEGE — Mon, 22 Sep 2025 23:51:02 -0500

termal, a fast, interactive, terminal-based viewer for multiple sequence alignments (MSAs), designed for use on remote systems such as high-performance computing (HPC) clusters.

https://academic.oup.com/bioinformaticsadvances/advance-article/doi/10.1093/bioadv/vbaf208/8257678?login=true

Address of the bookmark: https://github.com/sib-swiss/termal

SMASH: An alignment-free tool to find and visualise rearrangements between pairs of DNA sequences

Jit — Thu, 21 Dec 2017 08:26:57 -0600

SMASH is a completely alignment-free method to find and visualise rearrangements between pairs of DNA sequences. The detection is based on relative compression, namely using a FCM, also known as Markov model, of high context order (typically 20). The method has been approached with a tool (also called SMASH). For visualization, SMASH outputs a SVG image, with an ideogram output architecture, where the patterns are represented with several HSV values (only value varies). The following image, illustrating the information maps between human and chimpanzee for the several chromosomes, depicts an example:

Address of the bookmark: https://github.com/pratas/smash

D-GENIES: A tool for Dotplot large Genomes in an Interactive, Efficient and Simple way

Jit — Mon, 11 Jun 2018 09:41:22 -0500

D-GENIES – for Dotplot large Genomes in an Interactive, Efficient and Simple way – is an online tool designed to compare two genomes. It supports large genome and you can interact with the dot plot to improve the visualisation. We use minimap version 2 to align the two genomes. Then, the PAF file is parsed and plotted into an interactive plot written with d3.js library. D-Genies also allows to display dot plots from other aligners by uploading their PAF or MAF alignment file. http://dgenies.toulouse.inra.fr/

Address of the bookmark: http://dgenies.toulouse.inra.fr/

Miropeats: discovers regions of sequence similarity amongst any set of DNA sequences

Poonam Mahapatra — Mon, 26 Aug 2019 17:55:24 -0500

Miropeats discovers regions of sequence similarity amongst any set of DNA sequences and then presents this similarity information graphically. Sequence similarity searching is a very general tool that forms the basis of many different biological sequence analyses but it is limited by the verbosity of traditional alignment presentation styles. Miropeats enhances the utility of conventional DNA sequence comparisons when looking at long lengths of sequence similarity by summarizing extensive large scale sequence similarities on a single page of graphics. The latest version of Miropeats can be used as a general pairwise alignment program or in its traditional role sorting out a big mess of overlapping or similar regions.

Address of the bookmark: http://www.littlest.co.uk/software/bioinf/old_packages/miropeats/

MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons

Jit — Mon, 18 Feb 2019 04:21:50 -0600

MACSE aligns coding NT sequences with respect to their AA translation while allowing NT sequences to contain multiple frameshifts and/or stop codons. MACSE is hence the first automatic solution to align protein-coding gene datasets containing non-functional sequences (pseudogenes) without disrupting the underlying codon structure. It has also proved useful in detecting undocumented frameshifts in public database sequences and in aligning next-generation sequencing reads/contigs against a reference coding sequence.

For further details about the underlying algorithm see the original publication:
MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons.
Vincent Ranwez, Sébastien Harispe, Frédéric Delsuc, Emmanuel JP Douzery
PLoS One 2011, 6(9): e22594.

Address of the bookmark: https://bioweb.supagro.inra.fr/macse/index.php?menu=releases

Sequence Tube Maps: displays multiple genomic sequences in the form of a tube map

Jit — Wed, 11 Mar 2020 01:12:06 -0500

A JavaScript module for the visualization of genomic sequence graphs. It automatically generates a "tube map"-like visualization of sequence graphs which have been created with vg. (https://github.com/vgteam/vg)

Link to working demo: https://vgteam.github.io/sequenceTubeMap/

Address of the bookmark: https://github.com/vgteam/sequenceTubeMap

Pacman

Rahul Nayak — Mon, 16 Feb 2015 12:15:17 -0600

The pacman package is an R package management tool that combines the functionality of base library related functions into intuitively named functions. This package is ideally added to .Rprofile to increase workflow by reducing time recalling obscurely named functions, reducing code and integrating functionality of base functions to simultaneously perform multiple actions.

Function names in the pacman package follow the format of p_xxx where ‘xxx’ is the task the function performs. For instance the p_load function allows the user to load one or more packages as a more generic substitute for the library or require functions and if the package isn’t available locally it will install it for you.

Installation

To download the development version of pacman:

Download the zip ball or tar ball, decompress and run R CMD INSTALL on it, or use the devtools package to install the development version:

## Make sure your current packages are up to date
update.packages()
## devtools is required
devtools::install_github("trinker/pacman")

Note: Windows users need Rtools and devtools to install this way.

More at https://github.com/trinker/pacman