BOL: Related items

ShRec3D

Jitendra Narayan — Thu, 25 Dec 2014 23:14:52 -0600

ShRec3D is a program that aims at reconstructing a genome 3D structure (b) from the sole knowledge of the contacts between different genomic regions (a) as determined by Hi-C (http://www.ncbi.nlm.nih.gov/pubmed/19815776).

There are two options to run ShRec3D (on linuX only so far): the first one uses the Matlab complier runtime environment (MCR), the second one doesn't need any other library to be installed but only works with the latest versions of Linux (equivalent to Fedora 19 and above).

Address of the bookmark: https://sites.google.com/site/julienmozziconacci/#TOC-Downloads

Sequencing By Xpansion

Jitendra Narayan — Wed, 17 Jun 2015 20:58:11 -0500

Sequencing By Xpansion (SBX) is a DNA sequencing method that uses a simple biochemical reaction to encode the sequence of a DNA molecule into a highly measurable surrogate called an Xpandomer. This single molecule approach produces enough Xpandomer in a single drop reaction to sequence an entire human genome 1000X over. To achieve this, an Xpandomer replaces each DNA sequence with a sequence of large, high signal reporter molecules using the SBX molecular expansion technology. The DNA sequence is then read out as the Xpandomer reporters pass sequentially through a nanopore detector. SBX is a molecular engineering platform that benefits from core design principles that separate the multiple molecular functions. This systems approach enables efficient development and incorporation of improvements to SBX and is key to reconfiguring and optimizing Xpandomer measurement for different detection platforms.

http://www.stratosgenomics.com/stratos-genomics-technology

Katju Lab

Fri, 26 Feb 2016 03:25:32 -0600

TheLab seek to understand the genetic factors contributing to genomic variation and phenotypic diversity. To this end, we employ molecular and bioinformatic tools to study evolutionary processes at the level of populations, both experimental and natural, and genomes. Our research interests encompass a wide range of topics, including the evolution of organellar and nuclear genomes, gene duplication and the origin of novel function, and the fitness and phenotypic consequences of mutation in evolution. For details regards ongoing projects, please see the Research page.

http://katjulab.com/research.html

BUSCO

Jitendra Narayan — Sun, 07 Feb 2016 16:02:39 -0600

Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs

More at http://busco.ezlab.org/

Address of the bookmark: http://busco.ezlab.org/

Genome Browser : GBrowse

Jit — Fri, 19 Feb 2016 09:22:43 -0600

Generic Genome Browser Version 2: A Tutorial for Administrators

This is an extensive tutorial to take you through the main features and gotchas of configuring GBrowse as a server. This tutorial assumes that you have successfully set up Perl, GD, BioPerl and the other GBrowse dependencies. If you haven't, please see the GBrowse HOWTO During most of the tutorial, we will be using the "in-memory" GBrowse database (no relational database required!) Later we will show how to set up a genome size database using the berkeleydb and MySQL adaptors.

More at http://elp.ucdavis.edu/tutorial/tutorial.html

Address of the bookmark: http://elp.ucdavis.edu/tutorial/tutorial.html

RCircos: an R package for Circos 2D track plots

Jit — Fri, 20 May 2016 11:01:13 -0500

RCircos package provides a simple and flexible way to make Circos 2D track plots with R and could be easily integrated into other R data processing and graphic manipulation pipelines for presenting large-scale multi-sample genomic research data. It can also serve as a base tool to generate complex Circos images.

More at https://bitbucket.org/henryhzhang/rcircos/src

Address of the bookmark: https://bitbucket.org/henryhzhang/rcircos/src

SRF Bioinformatics job position in National Institute of Plant Genome Research (NIPGR)

Mon, 19 Sep 2016 05:43:38 -0500

SRF Bioinformatics job position in National Institute of Plant Genome Research (NIPGR)
Title : “Transcriptome and small RNA diversity analysis of developing seed contrasting rice varieties”
Qualification : Candidates having M.Sc./M.Tech. degree or equivalent (with minimum 60% marks) in Bioinformatics with a minimum of two years of post M.Sc./M.Tech research experience are eligible to apply.
No. of Post : 01
How to apply
Application should reach to Dr. Pinky Agarwal, Staff Scientist, National Institute of Plant Genome Research (NIPGR) Aruna Asaf Ali Marg, P.O. Box NO. 10531, New Delhi - 110067 on or before 30/09/2016

More at http://www.nipgr.res.in/careers/vacancies_latest.php#

Strudel

Anjana — Fri, 30 Sep 2016 09:47:02 -0500

Strudel is our graphical tool for visualizing genetic and physical maps of genomes for comparative purposes. The application aims to let the user examine their data at a variety of different levels of resolution, from entire maps to individual markers, and explore syntenic relationships between genomes. All browsing and interaction with Strudel happens in real-time – there is no need to wait while the maps are generated. It is built using Java 1.6 and ships with its own JRE, so there is no need for users to install or update Java.

Address of the bookmark: https://ics.hutton.ac.uk/strudel/

MIRO : miRNA omics

Jit — Tue, 04 Oct 2016 14:50:48 -0500

The MIRO (the miRNA omics) pipeline is a flexible and powerful tool for the analysis of miRNA (or more generall short RNA) expression using short-read deep sequencing data. In its present implementation MIRO is especially adapted for the analysis of reads generated with the Illumina sequencing platform. MIRO allows to preprocess the Solexa-reads, map them flexibly to several reference genomes using one of four different mappers, create differential gene (miRNA) expression profiles and cluster reads using one of several algorithm. MIRO output is furthermore compatible with software such as genome browsers and miRDeep.

Address of the bookmark: http://seq.crg.es/download/software/Miro/

Understanding Greedy Algorithms

Jit — Mon, 12 Dec 2016 04:37:40 -0600

Learning greedy algo for biologist.

https://www.topcoder.com/community/data-science/data-science-tutorials/greedy-is-good/

This webpage is also useful for the same:

http://learninglover.com/examples.php?id=59

http://www.cs.rpi.edu/~magdon/ps/conference/super_biokdd.pdf

https://ocw.mit.edu/courses/biology/7-91j-foundations-of-computational-and-systems-biology-spring-2014/lecture-slides/MIT7_91JS14_Lecture6.pdf

http://schatzlab.cshl.edu/teaching/AssemblyClass/01.%20Assembly%20Intro.pdf

http://lsl.sinica.edu.tw/Services/Class/files/20150612449.pdf

http://www.cs.jhu.edu/~langmea/resources/lecture_notes/assembly_scs.pdf

https://www2.eecs.berkeley.edu/Pubs/TechRpts/2016/EECS-2016-43.pdf

Address of the bookmark: https://www.topcoder.com/community/data-science/data-science-tutorials/greedy-is-good/