BOL: Related items

Bio7: an integrated development environment for ecological modeling, scientific image analysis and statistical analysis

Nidhi Rajput — Fri, 07 Feb 2020 23:32:24 -0600

The application Bio7 is an integrated development environment for ecological modeling, scientific image analysis and statistical analysis. The application itself is based on an RCP-Eclipse-Environment (Rich-Client-Platform) which offers a huge flexibility in configuration and extensibility because of its plug-in structure and the possibility of customization.

https://bio7.org/about/

Address of the bookmark: https://bio7.org/home-2/

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/

poRe: an R package for the visualization and analysis of nanopore sequencing data

Jit — Thu, 23 Nov 2017 09:55:57 -0600

Motivation: The Oxford Nanopore MinION device represents a unique sequencing technology. As a mobile sequencing device powered by the USB port of a laptop, the MinION has huge potential applications. To enable these applications, the bioinformatics community will need to design and build a suite of tools specifically for MinION data.

Results: Here we present poRe, a package for R that enables users to manipulate, organize, summarize and visualize MinION nanopore sequencing data. As a package for R, poRe has been tested on Windows, Linux and MacOSX. Crucially, the Windows version allows users to analyse MinION data on the Windows laptop attached to the device.

Availability and implementation: poRe is released as a package for R at http://sourceforge.net/projects/rpore/ . A tutorial and further information are available at https://sourceforge.net/p/rpore/wiki/Home/

Contact:mick.watson@roslin.ed.ac.uk

Address of the bookmark: https://academic.oup.com/bioinformatics/article/31/1/114/2365693

netGO: R-Shiny package for network-integrated pathway enrichment analysis

Jit — Wed, 12 Feb 2020 12:40:54 -0600

netGO is an R/Shiny package for network-integrated pathway enrichment analysis.
netGO provides user-interactive visualization of enrichment analysis results and related networks.

Currently, netGO supports analysis for four species (Human, Mouse, Arabidopsis thaliana,and Yeast)
These data are available from netGO-Data repository.

https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa077/5728635

Address of the bookmark: https://github.com/unistbig/netGO

kebabs: package provides functionality for kernel based analysis of biological sequences via Support Vector Machine (SVM) based methods

Rahul Nayak — Fri, 04 Mar 2022 00:14:11 -0600

The kebabs package provides functionality for kernel based analysis of biological sequences via Support Vector Machine (SVM) based methods. Biological sequences include DNA, RNA, and amino acid (AA) sequences. Sequence kernels define similarity measures between sequences. The package implements some of the most important kernels for sequence analysis in a very flexible and efficient way and extends the standard position-independent functionality of these kernels in a novel way to take the position of patterns in the sequences into account for the similarity measure.

http://www.bioinf.jku.at/software/kebabs/

http://bioconductor.org/packages/release/bioc/vignettes/kebabs/inst/doc/kebabs.pdf

Address of the bookmark: http://www.bioinf.jku.at/software/kebabs/

SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis

BioStar — Mon, 17 Aug 2020 05:21:09 -0500

SHAMAN is a shiny application for differential analysis of metagenomic data (16S, 18S, 23S, 28S, ITS and WGS) including bioinformatics treatment of raw reads for targeted metagenomics, statistical analysis and results visualization with a large variety of plots (barplot, boxplot, heatmap, …).
The bioinformatics treatment is based on Vsearch [Rognes 2016] which showed to be both accurate and fast [Wescott 2015].The statistical analysis is based on DESeq2 R package [Anders and Huber 2010] which robustly identifies the differential abundant features as suggested in [McMurdie and Holmes 2014] and [Jonsson2016]. SHAMAN robustly identifies the differential abundant genera with the Generalized Linear Model implemented in DESeq2 [Love 2014].
SHAMAN is compatible with standard formats for metagenomic analysis (.csv, .tsv, .biom) and figures can be downloaded in several formats. A presentation about SHAMAN is available here and a poster here.

More at https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03666-4

Address of the bookmark: https://github.com/aghozlane/shaman

You and your friend have similar DNA !!!

Jit — Sun, 27 Jul 2014 20:44:05 -0500

New research out of Massachusetts claims that people often choose friends that are similar to them in genetics and they are more accurate than you might suppose. A study published on PNAS http://www.pnas.org/content/111/Supplement_3/10796.full found that people are apt to pick friends who are genetically similar to themselves - so much so that friends tend to be as alike at the genetic level as a person's fourth cousin.

Scientists with a long-running Framingham Heart Study looked at 1,932 people (examination of about 1.5 million markers of genetic variations), comparing unrelated friends to unrelated strangers. They found that friends shared about 1% of their genes — a percentage much higher than those shared with strangers.This new findings made it clear that people have more DNA in common with those who are selected as friends than with strangers in the same population.

The genes that lined up the most were olfactory genes, which deal with smell. The ones that lined up the least were immune system genes. The researchers weren't sure why that happened :/. Olfactory genes might be a straightforward explanation: People who like the same smells tend to be drawn to similar environments, where they meet others with the same tendencies.

Reference:

http://www.pnas.org/content/111/Supplement_3/10796.full

Image : http://i.kinja-img.com

AccNET

Jitendra Narayan — Fri, 07 Oct 2016 05:22:11 -0500

AccNET is a Perl application that presents a new way to study the accessory genome of a given set of organisms. Using the proteomes of these organisms, AccNET create a bipartite network compatible with common network analysis platforms. AccNET collects phylogenetic and functional information in a network improving the analysis capability. Networks offer a new perspective of organism organization through elements acquired by horizontal gene transfers and not constricted by hierarchical structures.

More at https://www.youtube.com/watch?v=vdGuy1GAJrQ

Address of the bookmark: https://sourceforge.net/projects/accnet/

A5-miseq

Jit — Thu, 18 Aug 2016 04:05:23 -0500

_A5-miseq_ is a pipeline for assembling DNA sequence data generated on the Illumina sequencing platform. This README will take you through the steps necessary for running _A5-miseq_.

Point to note:

There are many situations where A5-miseq is not the right tool for the job. In order to produce accurate results, A5-miseq requires Illumina data with certain characteristics. A5-miseq will likely not work well with Illumina reads shorter than around 80nt, or reads where the base qualities are low in all or most reads before 60nt. A5-miseq assumes it is assembling homozygous haploid genomes. Use a different assembler for metagenomes and heterozygous diploid or polyploid organisms. Use a different assembler if a tool like FastQC reports your data quality is dubious. You have been warned! Datasets consisting solely of unpaired reads are not currently supported.

Address of the bookmark: https://sourceforge.net/projects/ngopt/

Bioinformatics tools and software

Jit — Tue, 05 Jul 2016 10:02:26 -0500

USEARCH >
Extreme high-throughput sequence analysis. Orders of magnitude faster than BLAST. MUSCLE >
Multiple sequence alignment. Faster and more accurate than CLUSTALW.

UPARSE >
OTU clustering for 16S and other marker genes. Highly accurate OTU sequences and improved diversity measures. UCHIME >
Chimeric sequence detection. PILER >
De novo genome repeat finder. PILER-CR >
Detection of CRISPR repeats in bacterial genomes. QSCORE >
Compare two multiple alignments for benchmarking. PALS >
Whole-genome alignment. PREFAB >
Protein Reference Alignment Database. MSA benchmark collection >
Selected multiple alignment benchmarks in a standardized FASTA format.

Address of the bookmark: http://drive5.com/software.html