BOL: Related items

BEDOPS v2.4.26: high-performance genomic feature operations

Jit — Mon, 12 Jun 2017 10:11:01 -0500

BEDOPS v2.4.26 is a suite of tools to address common questions raised in genomic studies — mostly with regard to overlap and proximity relationships between data sets. It aims to be scalable and flexible, facilitating the efficient and accurate analysis and management of large-scale genomic data.

The overview section of the BEDOPS v2.4.26 documentation summarizes the toolkit, functionality and performance enhancements. The reference table offers documentation for all applications and scripts.

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

MGcV: the microbial genomic context viewer for comparative genome analysis

Jit — Mon, 29 Jan 2018 04:55:46 -0600

MGcV is an interactive web-based visalization tool tailored to facilitate small scale genome analysis. To start using MGcV:

Supply your genes/genomic segments/phylogenetic tree of interest in the input-box by
- selecting the type of identifier and pasting identifiers (one per line)
- or by using the gene ID search tool
- or with the BLAST search tool
Click "Visualize context".

Consult the documentation to learn more about MGcV.

Address of the bookmark: http://mgcv.cmbi.ru.nl/

RestrictionDigest: A powerful Perl module for simulating genomic restriction digests

Neel — Tue, 12 Jun 2018 13:17:13 -0500

RestrictionDigest can simulate the reference genome digestion and generate comprehensive information of the simulation. It can simulate single-enzyme digestion, double-enzyme digestion and size selection process. It can also analyze multiple genomes at one run and generates concise comparison of enzyme(s) performance across the genomes. For more information, please see the academic paper published online (http://www.sciencedirect.com/science/article/pii/S071734581630001X).

Address of the bookmark: https://github.com/JINPENG-WANG/RestrictionDigest

regioneR: an R package for the management and comparison of genomic regions

Jit — Tue, 11 Dec 2018 08:43:51 -0600

Regioner is an R package for the management and comparison of genomic regions. It offers a set of function for basic manipulation of region sets extending the functionality of GenomicRanges and a powerful and customizable permutation test framework. With it, it's possible to study the association of a set of regions with other sets of regions, functions defined over the genome or essentially any user defined function.

http://gattaca.imppc.org/regioner/

Address of the bookmark: http://gattaca.imppc.org/regioner/

Apollo: First instantaneous, collaborative genomic annotation editor available on the Web

Jit — Fri, 31 May 2019 19:55:39 -0500

Apollo is a plug-in for the JBrowse Genome Viewer.
In addition to genes and pseudogenes, users can annotate ncRNAs (snRNA, snoRNA, tRNA, rRNA), miRNAs, repeat regions, and transposable elements; each annotation type has its own configuration of the ‘Information Editor’.
History tracking with undo/redo functions is available.
Users are able to directly set an annotation to a specific state, choosing from the ‘History’ display.
Adding and updating PubMed IDs will prompt users with a publication title to confirm their submission.
Gene Ontology (GO) terms are supported and GO ID auto-completion has been incorporated.
Users may access a ‘Recent Changes’ page.
Help page with Apollo specific content is available.

Address of the bookmark: http://genomearchitect.github.io/

Phytozome v12.1: plant science community hub for accessing palnts genomic data

Surabhi Chaudhary — Tue, 17 Mar 2020 07:30:17 -0500

Phytozome, the Plant Comparative Genomics portal of the Department of Energy's Joint Genome Institute, provides JGI users and the broader plant science community a hub for accessing, visualizing and analyzing JGI-sequenced plant genomes, as well as selected genomes and datasets that have been sequenced elsewhere. As of release v12.1.6, Phytozome hosts 93 assembled and annotated genomes, from 82 Viridiplantae species. More than half of these genomes have been sequenced, assembled and/or annotated with JGI Plant Science program resources. By integrating this large collection of plant genomes into a single resource and performing comprehensive and uniform annotation and analyses, Phytozome facilitates accurate and insightful comparative genomics studies.

Address of the bookmark: https://phytozome.jgi.doe.gov/pz/portal.html

GenoFig: a user-friendly application for the visualization and comparison of genomic regions

BioStar — Mon, 05 Aug 2024 23:06:58 -0500

Tool for graphical vizualisation of annotated genetic regions, and homologous regions comparison. It is an independent recoding of Easyfig 2 initially developped by at the S. Beatson Lab [https://mjsull.github.io/Easyfig/]

Download the GenoFig source code using the 'Download' button on top of this page. Cloning is currently not available for people not member of the INRAE French Institution. After decompression, open a terminal in the folder containing the decompressed files and run:

conda env create -f extras/requirements.yml
extras/SETUP.sh

Address of the bookmark: https://forgemia.inra.fr/public-pgba/genofig

RITA: Rapid identification of high-confidence taxonomic assignments for metagenomic data

Jit — Mon, 27 Nov 2017 08:25:33 -0600

RITA is a standalone software package and Web server for taxonomic assignment of metagenomic sequence reads. By combining homology predictions from BLAST or UBLAST with compositional classifications from a Naive Bayes classifier, RITA is able to achieve very high accuracy on short reads. Unlike other hybrid approaches which combine these predictions for all sequences to be classified, RITA uses a pipeline to first identify cases where both types of classifier are in agreement, which constitute the highest-confidence set. Sequences not classified in this manner are subjected to a series of downstream classification steps.

This work has been accepted for publication:

MacDonald NJ, Parks DH, and Beiko RG. Rapid identification of taxonomic assignments. Accepted to Nucleic Acids Research April 4, 2012.

If you have any questions or bug reports, please let us know at .

Address of the bookmark: http://kiwi.cs.dal.ca/Software/RITA

ITIS: the Integrated Taxonomic Information System!

Jit — Fri, 30 Aug 2019 23:07:15 -0500

ITIS, the Integrated Taxonomic Information System! Here you will find authoritative taxonomic information on plants, animals, fungi, and microbes of North America and the world. We are a partnership of U.S., Canadian, and Mexican agencies (ITIS-North America); other organizations; and taxonomic specialists. ITIS is also a partner of Species 2000 and the Global Biodiversity Information Facility (GBIF). The ITIS and Species 2000 Catalogue of Life (CoL)partnership is proud to provide the taxonomic backbone to the Encyclopedia of Life (EOL).

https://www.itis.gov/pdf/twb_ug.pdf

Address of the bookmark: https://www.itis.gov/