BOL: Related items

NCBI Remap

Jit — Thu, 11 Feb 2016 11:02:26 -0600

NCBI Remap. This tool is conceptually similar to liftOver in that in manages conversions between a pair of genome assemblies but it uses different methods to achieve these mappings. It is also available through a simple web interface or you can use the API for NCBI Remap.

More at http://www.ncbi.nlm.nih.gov/genome/tools/remap

API http://www.ncbi.nlm.nih.gov/genome/tools/remap/docs/api

Address of the bookmark: http://www.ncbi.nlm.nih.gov/genome/tools/remap

Des Higgins: Visualizing Multiple Sequence Alignments

Wed, 26 Feb 2014 00:50:08 -0600

Copyright Broad Institute, 2013. All rights reserved. Des Higgins (http://www.bioinf.ucd.ie) gives a very entertaining introduction to the visualization of multiple sequence alignment, and to his widely-used Clustal tool. He highlights the emerging challenge of managing alignments with a very large number of sequences, and presents several approaches to this challenge, including faster algorithms and abstract views of clusters of alignments. This talk was presented at VIZBI 2011, an international conference series on visualizing biological data (http://www.vizbi.org) funded by NIH & EMBO. For information about data visualization efforts at the Broad Institute, please visit: http://www.broadinstitute.org/node/1363/

Przeworski lab

Mon, 15 Feb 2016 05:41:54 -0600

Genetic differences among individuals reflect the combined effects of mutation, recombination, population history and natural selection. As a result, studies of natural variation can provide important insights into evolutionary and genetic mechanisms: as examples, DNA sequence conservation among distantly related species can help identify functional roles too subtle to be detected in lab settings, while analyses of population variation allow for inferences about events that are too infrequent to be measured directly. Our research employs this general approach to learn about the dynamics of adaptation and the determinants of recombination and mutation, in humans and in other species.

More at http://przeworski.c2b2.columbia.edu/

CrusView

Jit — Thu, 12 Apr 2018 09:22:03 -0500

CrusView is a java based tool for karyotype/genome visualization and comparison of crucifer Species. It also integrates an binary version of KGBassembler and a post-modification step for its assembling result.

Address of the bookmark: http://www.cmbb.arizona.edu/?page_id=250

BioToolbox

Jit — Fri, 19 Feb 2016 09:14:44 -0600

This is a collection of libraries and high-quality end-user scripts for bioinformatic analysis, including working with gene annotation, collecting data scores from a variety of modern file formats, and conversion between file formats. The Bio::ToolBox libraries provide a unified, abstracted interface to multiple common gene annotation formats and the collection of data from multiple data files. They rely on BioPerl SeqFeature libraries and related adaptors to access binary file formats including Bam, BigWig, BigBed, and USeq. The Bio::ToolBox package includes scripts for setting up databases of annotation, collecting annotated features, collecting genomic data relative to features, manipulating and analyzing data, and data format conversion.

More at http://cpansearch.perl.org/src/TJPARNELL/

Address of the bookmark: http://cpansearch.perl.org/src/TJPARNELL/

NAViGaTOR: Network Analysis, Visualization and Graphing Toronto

Rahul Nayak — Tue, 03 Jul 2018 05:05:55 -0500

NAViGaTOR – Network Analysis, Visualization, & Graphing TORonto is a software system for scaleable visualizing and analyzing networks. The current version, NAViGaTOR 3, increases modularity, improves scaleability, extends input/output options, brings new network views and analysis algorithms. http://142.150.188.236/navigatorwp/

Address of the bookmark: http://142.150.188.236/navigatorwp/

RA at ICAR - INDIAN INSTITUTE OF OILSEEDS RESEARCH

Mon, 22 Feb 2016 05:21:34 -0600

ICAR - INDIAN INSTITUTE OF OILSEEDS RESEARCH

HYDERABAD-500030

F.No. 5-42/2016/Rectt.

WALK IN INTERVIEW

Eligible candidates are invited to attend Walk in Interview to fill up the (purely) temporary post of Junior Research Fellow (One) under Extramural Research Project entitled “Transcriptome and proteome analysis for identification of candidate genes responsible for pistillate nature in castor “ to be held on 04.03.2016 at 11.00 AM at ICAR – Indian Institute of Oilseeds Research, Rajendranagar, Hyderabad. The tenure of the project is up to 31.03.2017. The requirement and other terms and conditions for the Junior Research Fellow are as under :-

Junior Research Fellow (One)

Nucleic acid isolations, molecular analysis, bioinformatic analysis

.M.Sc.Biotechnology/Bioinformatics

Post Graduation in Life Sciences.

Candidates having Post Graduate degree in Basic Sciences with 3 years Bachelor’s degree and 2 years Master’s Degree 1,2,3 should have NET qualification.

Experience in Plant Biotechnology and Bioinformatics

Rs.25000/- + 30% HRA per month (At present)

More Info : http://icar-iior.org.in/media/docs/employment/2016/jrf-int.pdf

Juicebox: Visualization and analysis software for Hi-C data

Jit — Fri, 21 Feb 2020 00:33:38 -0600

Juicebox is visualization software for Hi-C data. This distribution includes the source code for Juicebox, Juicer Tools, and Assembly Tools. Download Juicebox here, or use Juicebox on the web. Detailed documentation is available on the wiki. Instructions below pertain primarily to usage of command line tools and the Juicebox jar files.

Juicebox can now be used to visualize and interactively (re)assemble genomes. Check out the Juicebox Assembly Tools Module website https://aidenlab.org/assembly for more details on how to use Juicebox for assembly.

GUI at https://aidenlab.org/juicebox/

Address of the bookmark: https://github.com/aidenlab/Juicebox

destruct

Jitendra Prajapati — Mon, 29 Feb 2016 17:34:59 -0600

Destruct is a tool for joint prediction of rearrangement breakpoints from single or multiple tumour samples.

More at https://bitbucket.org/dranew/destruct

Address of the bookmark: https://bitbucket.org/dranew/destruct

Circleator

Jit — Sun, 25 Jun 2017 18:04:32 -0500

The Charm City Circleator--or Circleator for short--is a Perl-based visualization tool developed at the Institute for Genome Sciences in the University of Maryland's School of Medicine. Circleator produces circular plots of genome-associated data, like this one:

Common uses of the tool include:

Displaying the sequence and/or genes in a GenBank flat file.
Highlighting differences and/or similarities in gene content between related organisms.
Comparing SNPs and indels between closely-related strains or serovars.
Comparing gene expression values across multiple samples or timepoints.
Visualizing coverage plots of RNA-Seq read alignments.

Key Features

Circleator...

Builds on BioPerl and the input file formats that it supports, including:
- GenBank flat files, GFF, FASTA
Accepts a number of other commonly-used datatypes and file formats:
- BSR and TRF output, SAM/BAM files, VCF-encoded SNPs, tab-delimited files
Outputs publication-ready figures in the SVG (Scalable Vector Graphics) format.
Requires only a single configuration file whose layout mirrors that of the figure itself.
- Predefined configuration files and "track" types are supplied for common datasets.
- Advanced features allow limited analyses to be performed as a figure is drawn.
Includes an extensive set of regression tests.
Offers a prototype web-based GUI (under the "Ringmaster" project.)

https://github.com/jonathancrabtree/Circleator

Address of the bookmark: https://github.com/jonathancrabtree/Circleator