BOL: BioStar's bookmarks

PyParanoid: a pipeline for rapid identification of homologous gene families in a set of genomes

BioStar — Thu, 13 Aug 2020 10:06:19 -0500

PyParanoid is a pipeline for rapid identification of homologous gene families in a set of genomes - a central task of any comparative genomics analysis. The "gold standard" for identifying homologs is to use reciprocal best hits (RBHs) which depends on performing a all-vs-all sequence comparison, usually using BLAST, to determine homology. However, these methods are computationally expensive, requiring O(n2) resources to identify RBHs. This is problematic, as the modern deluge of sequencing data means that comparative genomics analyses could be performed on datasets of thousands of strains.

Address of the bookmark: https://github.com/ryanmelnyk/PyParanoid

PANNZER: a fully automated service for functional annotation of prokaryotic and eukaryotic proteins of unknown function.

BioStar — Thu, 13 Aug 2020 09:57:24 -0500

PANNZER (Protein ANNotation with Z-scoRE) is a fully automated service for functional annotation of prokaryotic and eukaryotic proteins of unknown function.

PANNZER (Protein ANNotation with Z-scoRE) is a fully automated service for functional annotation of prokaryotic and eukaryotic proteins of unknown function. The tool is designed to predict the functional description (DE) and GO classes.

PANNZER2 processes bacterial proteomes in minutes and eukaryotic proteomes in an hour. You can use AAI-profiler to summarize a proteome's species neighbors and reveal taxonomic identity or contamination.

Address of the bookmark: http://ekhidna2.biocenter.helsinki.fi/sanspanz/#

SEASTAR: Systematic Evaluation of Alternative STArt site in RNA

BioStar — Thu, 13 Aug 2020 09:54:27 -0500

SEASTAR (Systematic Evaluation of Alternative STArt site in RNA) is a software package for Transcription Start Site (TSS) identification and quantification using only RNA-seq data. It assembles novel TSSs based only on RNA-Seq data and merges them with known TSSs from a public database. This package enables high-quality TSS identification that is comparable to the highly sophisticated CAGE technology. This package is particularly useful for finding novel TSSs that contribute to transcriptome complexity along with identifying differential promoter utilization.

version 1.0.0 - updates several descriptions and tests. To achieve v0.9.4, one can visit https://github.com/zhyqin/SEASTAR-0.9.4 for download.

Address of the bookmark: https://github.com/Xinglab/SEASTAR

PheWAS: R package is designed to provide an accessible interface to the phenome wide association study

BioStar — Thu, 30 Jul 2020 22:06:37 -0500

The PheWAS R package is designed to provide an accessible interface to the phenome wide association study. For a description of the methods available and some simple examples, please see the package vignette or the R documentation. For installation help, see below. ##Installing the PheWAS Package The PheWAS package can be installed using the devtools package. The following code when executed in R will get you started:

install.packages("devtools")
#It may be necessary to install required as not all package dependencies are installed by devtools:
install.packages(c("dplyr","tidyr","ggplot2","MASS","meta","ggrepel","DT"))
devtools::install_github("PheWAS/PheWAS")
library(PheWAS)

Address of the bookmark: https://github.com/PheWAS/PheWAS

Sequence Ontology Bioinformatics Analysis (SOBA) tool to provide a simple statistical and graphical summary of an annotated genome

BioStar — Wed, 22 Jul 2020 10:11:13 -0500

We have developed the Sequence Ontology Bioinformatics Analysis (SOBA) tool to provide a simple statistical and graphical summary of an annotated genome. We envisage its use during annotation jamborees, genome comparison and for use by developers for rapid feedback during annotation software development and testing. SOBA also provides annotation consistency feedback to ensure correct use of terminology within annotations, and guides users to add new terms to the Sequence Ontology when required. SOBA is available at http://www.sequenceontology.org/cgi-bin/soba.cgi.

More at https://pubmed.ncbi.nlm.nih.gov/20494974/

Address of the bookmark: http://www.sequenceontology.org/cgi-bin/soba.cgi

The wavefront alignment (WFA) algorithm

BioStar — Sun, 28 Jun 2020 10:17:50 -0500

The wavefront alignment (WFA) algorithm is an exact gap-affine algorithm that takes advantage of
homologous regions between the sequences to accelerate the alignment process. As opposed to traditional dynamic programming algorithms that run in quadratic time, the WFA runs in time O(ns), proportional to the read length n and the alignment score s, using O(s^2) memory. Moreover, the WFA exhibits simple data dependencies that can be easily vectorized, even by the automatic features of modern compilers, for different architectures, without the need to adapt the code.

Address of the bookmark: https://github.com/smarco/WFA

VirtualFlow: a versatile, parallel workflow platform for carrying out virtual screening

BioStar — Sat, 13 Jun 2020 13:03:09 -0500

related tasks on Linux-based computer clusters of any type and size which are managed by a batchsystem (such as SLURM).

Currently, there exist two versions of VirtualFlow, which are tailored to different types of tasks:

They use the same core technology regarding the workflow management and parallelization, and they can be used individually or in concert with each other. Additional versions are expected to arrive in the future.

https://github.com/VirtualFlow

https://www.nature.com/articles/s41586-020-2117-z?

Address of the bookmark: https://virtual-flow.org/

AutoDock Vina: an open-source program for doing molecular docking.

BioStar — Sat, 13 Jun 2020 07:55:56 -0500

AutoDock Vina is an open-source program for doing molecular docking. It was designed and implemented by Dr. Oleg Trott in the Molecular Graphics Lab at The Scripps Research Institute. It is especially effective for protein-ligand docking. AutoDock 4 is available under the GNU General Public License. AutoDock is one of the most cited docking software applications in the research community.

http://vina.scripps.edu/

Address of the bookmark: http://vina.scripps.edu/

gggenes: a ggplot2 extension for drawing gene arrow maps.

BioStar — Tue, 02 Jun 2020 11:43:34 -0500

Install the stable version of gggenes from CRAN:

install.packages("gggenes")

If you want the development version, install it from GitHub:

devtools::install_github("wilkox/gggenes")

More at https://github.com/wilkox/gggenes

Address of the bookmark: http://wilkox.org/gggenes

Genobuntu: Package for Next Generation Sequencing and Genome Assembly

BioStar — Mon, 18 May 2020 16:47:56 -0500

Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools.

Commonly used biological software and example script files for different assembly pipelines have also been provided, where the example script files can be updated to suit one’s experimental needs. Genobuntu attempts to reduce the amount of time and energy needed to build software workstations and it can also act as a good teaching source for a class room setting.

Therefore, Genobuntu offers a well-tailored environment for both novices and experts working in the field of genome assembly.

Features

Velvet
MiB
SSAKE
EULER
VCAKE
ABySS
ALLPATHS
Celera
SHARCGS
Allpaths
IDBA
TAIPAN
Edena
SOAPdenovo
Maq
IDBA-UD
No. of Reads present in the Ref. Seq.
ART NGS Reads Simulator
HiTEC, FASTQC
Minimum Description Length
SOAPaligner
Sequencing Read Archive Toolkit

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