BOL: Related items

OrthoGNC: A Software for Accurate Identification of Orthologs Based on Gene Neighborhood Conservation

Jit — Tue, 14 Nov 2017 09:30:35 -0600

Orthology relations can be used to transfer annotations from one gene (or protein) to another. Hence, detecting orthology relations has become an important task in the post-genomic era. Various genomic events, such as duplication and horizontal gene transfer, can cause erroneous assignment of orthology relations. In closely-related species, gene neighborhood information can be used to resolve many ambiguities in orthology inference. Here we present OrthoGNC, a software for accurately predicting pairwise orthology relations based on gene neighborhood conservation. Analyses on simulated and real data reveal the high accuracy of OrthoGNC. In addition to orthology detection, OrthoGNC can be employed to investigate the conservation of genomic context among potential orthologs detected by other methods. OrthoGNC is freely available online at http://bs.ipm.ir/softwares/orthognc and http://tinyurl.com/orthoGNC.

http://www.comp.nus.edu.sg/~wongls/projects/orthoGNC/

Address of the bookmark: http://www.sciencedirect.com/science/article/pii/S1672022917301663

HGT-Finder: A New Tool for Horizontal Gene Transfer Finding and Application to Aspergillus genomes

Jit — Wed, 17 Jan 2018 05:03:19 -0600

HGT-Finder:

(i) can be used for HGT detection in both prokaryotes and eukaryotes,

(ii) can report a statistical P value for each gene to indicate how likely it is to be horizontally transferred, and

(iii) is fully automated (requires minimal human intervention), as well as very easy to install and run.

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4626719/

BioGPS: Spotlight on the Gene Expression Atlas

Jit — Thu, 18 Oct 2018 12:15:12 -0500

BioGPS opened 2016 with a publication in Nucleic Acids Research, right after the New Year holiday. Throughout the year, new designs for the site were being created, reviewed, adjusted, reviewed, adjusted, and more review/adjustments in anticipation of a site redesign for 2017. A Plugin registration Blitz was held in March and April; followed by a Plugin Review Blitz in May. The BioGPS spotlight series was also restarted, with spotlights on BGEE, Intermine, and other Intermine-related plugins.

There were ~910,000 requests made to BioGPS in 2016. Requests to BioGPS peaked in March and at the lowest in December.

Address of the bookmark: http://biogps.org/

ShinyGO v0.61: Gene Ontology Enrichment Analysis + more

Jit — Wed, 03 Jun 2020 08:00:30 -0500

2/3/2020: Now published by Bioinformatics.

11/3/2019: V 0.61, Improve graphical visualization (thanks to reviewers). Interactive networks and much more.

5/20/2019: V.0.60, Annotation database updated to Ensembl 96. New bacterial and fungal genomes based on STRING-db! Just paste your gene list to get enriched GO terms and othe pathways for over 315 plant and animal species, based on annotation from Ensembl (Release 96), Ensembl plants (R. 43) and Ensembl Metazoa (R. 43). An additional 2031 genomes (including bacteria and fungi) are annotated based on STRING-db (v.10). In addition, it also produces KEGG pathway diagrams with your genes highlighted, hierarchical clustering trees and networks summarizing overlapping terms/pathways, protein-protein interaction networks, gene characterristics plots, and enriched promoter motifs.

Address of the bookmark: http://bioinformatics.sdstate.edu/go/

DarkHorse: a method for genome-wide prediction of horizontal gene transfer

Jit — Thu, 22 Jun 2017 07:58:35 -0500

A new approach to rapid, genome-wide identification and ranking of horizontal transfer candidate proteins is presented. The method is quantitative, reproducible, and computationally undemanding. It can be combined with genomic signature and/or phylogenetic tree-building procedures to improve accuracy and efficiency. The method is also useful for retrospective assessments of horizontal transfer prediction reliability, recognizing orthologous sequences that may have been previously overlooked or unavailable. These features are demonstrated in bacterial, archaeal, and eukaryotic examples.

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852411/

GeNeCK (Gene Network Construction Kit) is a comprehensive online tool kit that integrate various statistical methods to construct gene networks

Rahul Nayak — Tue, 15 Jan 2019 09:39:30 -0600

GeNeCK (Gene Network Construction Kit) is a comprehensive online tool kit that integrate various statistical methods to construct gene networks based on gene expression data and optional hub gene information.

It efficiently constructs gene networks from expression data. It allows the user to use ten different network construction methods (such as partial correlation-, likelihood-, Bayesian- and mutual information-based methods) and integrates the resulting networks from multiple methods. Hub gene information, if available, can be incorporated to enhance performance.

GeNeCK is an efficient and easy-to-use web application for gene regulatory network construction. It can be accessed at http://lce.biohpc.swmed.edu/geneck

Address of the bookmark: http://lce.biohpc.swmed.edu/geneck/

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

homologizer: Phylogenetic phasing of gene copies into polyploid subgenomes

Abhi — Sat, 03 Jun 2023 19:19:10 -0500

This tutorial describes the usage of homologizer to phase gene copies into polyploid subgenomes. The tutorial is an abbreviated version of a soon-to-be published paper in Methods in Molecular Biology. Please see that paper for many more details and practical considerations for running homologizer analyses. If you use homologizer, please cite the paper in which we first describe the method:

Freyman, W.A., Johnson, M.G., and C.J. Rothfels. 2022. Homologizer: phylogenetic phasing of gene copies into polyploid subgenomes. bioRxiv 2020.10.22.351486v4

homologizer is implemented in RevBayes. Please see http://revbayes.com to download and install RevBayes. For users without previous RevBayes experience, we recommend the tutorials at http://revbayes.com.

Address of the bookmark: https://github.com/wf8/homologizer

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/

UnCoVar: Workflow for Transparent and Robust Virus Variant Calling, Genome Reconstruction and Lineage Assignment

BioStar — Mon, 05 Aug 2024 23:01:29 -0500

UnCoVar: Workflow for Transparent and Robust Virus Variant Calling, Genome Reconstruction and Lineage Assignment

Using state of the art tools, easily extended for other viruses
Tool and database updates for critical components via Conda
Built using modern design patterns with Conda and Snakemake
Extensible and easy to customize
Submission Ready Genomes
Customizable reporting with comprehensive visualization

https://ikim-essen.github.io/uncovar/

Github https://github.com/IKIM-Essen/uncovar

Address of the bookmark: https://ikim-essen.github.io/uncovar/