BOL: Related items

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/

HiGlass: a tool for exploring genomic contact matrices and tracks.

Jit — Mon, 11 Jun 2018 09:44:49 -0500

HiGlass is a tool for exploring genomic contact matrices and tracks. Please take a look at the examples and documentation for a description of the ways that it can be configured to explore and compare contact matrices. To load private data, HiGlass can be run locally within a Docker container. The HiC data in the examples below is from Rao et al. (2014) http://higlass.io/

Address of the bookmark: http://higlass.io/

swgis v2.0 : a seqword genomic island sniffer

Abhimanyu Singh — Thu, 01 Nov 2018 12:35:52 -0500

swgis v2.0 is the modified version of the seqword genomic island sniffer. this version is specifically optimized for predicting genomic islands in eukaryotic genomes. swgis v2.0 was tested on several eukaryotic species of different lineages. all identified genomic islands were deposited in the eugi database.

download swgis v2.0

Address of the bookmark: http://eugi.bi.up.ac.za/eugi_download_swgis.php

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

Figeno: Tool for plotting sequencing data along genomic coordinates.

LEGE — Tue, 17 Sep 2024 02:28:15 -0500

Tool for plotting sequencing data along genomic coordinates.

FIGENO is a
  FIGure
    GENerator
for GENOmics

With figeno, you can plot various types of sequencing data along genomic coordinates. Video overview: https://www.youtube.com/watch?v=h1cBeXoSYTA.

Address of the bookmark: https://github.com/CompEpigen/figeno

SIMBA: a Genome Assembly Project Management System

Neel — Thu, 29 Nov 2018 08:52:25 -0600

SIMBA, SImple Manager for Bacterial Assemblies, is a Web interface for managing assembly projects of bacterial genomes. SIMBA was created to assist bioinformaticians to assemble bacterial genomes sequenced with NextGeneration Sequencing (NGS) platforms quickly, easily and effectively. SIMBA also is open source tool, i.e., can be freely downloaded, shared and modified.

Address of the bookmark: http://ufmg-simba.sourceforge.net/

scikit-bio™ is an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics.

Jit — Fri, 02 Mar 2018 04:29:47 -0600

scikit-bio is currently in beta. We are very actively developing it, and backward-incompatible interface changes can and will arise. To avoid these types of changes being a surprise to our users, our public APIs are decorated to make it clear to users when an API can be relied upon (stable) and when it may be subject to change (experimental). See the API stability docs for more details, including what we mean by stable and experimental in this context.

Address of the bookmark: http://scikit-bio.org/

modelStudio: a package automates the explanation of machine learning predictive models

Jit — Wed, 22 Jan 2020 23:58:11 -0600

The modelStudio package automates the explanation of machine learning predictive models. This package generates advanced interactive and animated model explanations in the form of a serverless HTML site.

It combines R with D3.js to produce plots and descriptions for various local and global explanations. Tools for model exploration unite with tools for EDA (Exploratory Data Analysis) to give a broad overview of the model behavior. modelStudio is a fast and condensed way to get all the answers without much effort. Break down your model and look into its ingredients with only a few lines of code.

Address of the bookmark: https://modeloriented.github.io/modelStudio/index.html

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/