BOL: Related items

ALF--a simulation framework for genome evolution.

Jit — Tue, 22 Oct 2019 22:05:58 -0500

Artificial Life Framework (ALF) simulates a root genome into a number of related genomes. Result files include the resulting gene sequences, true tree and true MSAs. A description of ALF can be found in the following article:

Daniel A Dalquen, Maria Anisimova, Gaston H Gonnet, Christophe Dessimoz: ALF - A Simulation Framework for Genome Evolution. Mol Biol Evol, 29(4):1115-1123, April 2012.
http://mbe.oxfordjournals.org/content/29/4/1115

Address of the bookmark: http://alfsim.org/#index

QuIN’s web server

Jit — Mon, 27 Jun 2016 10:44:16 -0500

Recent studies of the human genome have indicated that regulatory elements (e.g. promoters and enhancers) at distal genomic locations can interact with each other via chromatin folding and affect gene expression levels. Genomic technologies for mapping interactions between DNA regions, e.g., ChIA-PET and HiC, can generate genome-wide maps of interactions between regulatory elements. These interaction datasets are important resources to infer distal gene targets of non-coding regulatory elements and to facilitate prioritization of critical loci for important cellular functions. With the increasing diversity and complexity of genomic information and public ontologies, making sense of these datasets demands integrative and easy-to-use software tools. Moreover, network representation of chromatin interaction maps enables effective data visualization, integration, and mining. Currently, there is no software that can take full advantage of network theory approaches for the analysis of chromatin interaction datasets. To fill this gap, we developed a web-based application, QuIN, which enables: 1) building and visualizing chromatin interaction networks, 2) annotating networks with user-provided private and publicly available functional genomics and interaction datasets, 3) querying network components based on gene name or chromosome location, and 4) utilizing network based measures to identify and prioritize critical regulatory targets and their direct and indirect interactions.

AVAILABILITY: QuIN’s web server is available at http://quin.jax.org QuIN is developed in Java and JavaScript, utilizing an Apache Tomcat web server and MySQL database and the source code is available under the GPLV3 license available on GitHub:https://github.com/UcarLab/QuIN/.

Address of the bookmark: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004809

Sequencing Solutions to World Health

Rahul Agarwal — Thu, 29 Aug 2013 15:05:35 -0500

"New technology that quickly, easily and economically reveals the genomes of viruses and pathogens transforms public health and medicine."

Source: Life technologies

Address of the bookmark: http://www.lifetechnologies.com/global/en/home/communities-social/blog/blogs/sequencing-solutions-to-world-health.html?cid=social_blogseries_20130829_11098264

Genome Browsers

Rahul Agarwal — Fri, 16 Aug 2013 19:04:47 -0500

Genome Browser is the platform/database used for searching and retreiving sequences and annotation of genomes belong to various eukaryotes, prokaryotes, etc.

Following are the weblink for different available browsers:

http://www.ensembl.org/index.html

http://ensemblgenomes.org/

http://genome.ucsc.edu/

http://www.ncbi.nlm.nih.gov/genome

http://www.ebi.ac.uk/genomes/

http://flybase.org/

http://cmr.jcvi.org/tigr-scripts/CMR/CmrHomePage.cgi

http://www.sanger.ac.uk/resources/databases/

Two major breakthrough!!

Rahul Agarwal — Mon, 02 Sep 2013 10:18:11 -0500

"Scientists in Uruguay in colloboration with European partners sequenced the genome of the high-value Tannat grape, from which "the most healthy of red wines" are fermented.

A quick, $1 syphilis test in development by researchers from UNU-BIOLAC."

Source:

http://www.sciencedaily.com/releases/2013/09/130902101846.htm

http://www.eurekalert.org/pub_releases/2013-09/tca-ssg082613.php

Encode sequencing data freely available to download and use for academic means

Rahul Agarwal — Thu, 13 Mar 2014 18:18:08 -0500

In Encode, regulatory elements investigated via DNA hypersensitivity assays, assays of DNA methylation, and chromatin immunoprecipitation (ChIP) of proteins that interact with DNA, including modified histones and transcription factors, followed by sequencing (ChIP-Seq).

More information:

https://genome.ucsc.edu/ENCODE/pilot.html

Address of the bookmark: https://genome.ucsc.edu/ENCODE/

Tsetse Fly Genome sequenced

Rahul Agarwal — Fri, 25 Apr 2014 10:48:35 -0500

As it reported online today in Science, the team used several sequencing approaches to tackle the tsetse fly's 366 million base genome.

The current study, and companion articles slated to appear in PLOS One, PLOS Genetics, and PLOS Neglected Tropic Diseases, are the result of nearly 150 researchers based in 18 countries.

Source:

http://www.genomeweb.com/sequencing/international-team-sequences-tsetse-fly-genome

Science for Life Laboratory (SciLifeLab)-Sweden

Sat, 10 May 2014 06:22:30 -0500

Science for Life Laboratory (SciLifeLab) is a national center for molecular biosciences with focus on health and environmental research. The center combines frontline technical expertise with advanced knowledge of translational medicine and molecular bioscience. SciLifeLab is a national resource and a collaboration between four universities: Karolinska Institutet, KTH Royal Institute of Technology, Stockholm University and Uppsala University.

Webpage : https://www.scilifelab.se/about-us/
Opportunity: https://www.scilifelab.se/about-us/career/

miRNA database and tools

Rahul Agarwal — Mon, 09 Jun 2014 07:58:40 -0500

Since few years miRNA has shown to play important role in therapeutic related research and also known to play vital role in controlling gene expression specifically at transcriptional and post-transcription levels. Here are some important DBs and tools related with miRNA:

miRNA Sequencing data analysis : http://tools.genxpro.net/omiras/

miRNApath( R based tool) : http://www.bioconductor.org/packages/release/bioc/html/miRNApath.html

miRWalk DB : http://www.umm.uni-heidelberg.de/apps/zmf/mirwalk/

TargetScanHuman : http://www.targetscan.org/

RNAhybrid : http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/welcome.html

RNA22 predictor : http://cbcsrv.watson.ibm.com/rna22.html

miRNA predictor : http://www.microrna.org/microrna/home.do

Plant miRNA DB :http://bioinformatics.cau.edu.cn/PMRD/

miRBASE DB: http://www.mirbase.org/

Plant RNA predictor : http://plantgrn.noble.org/psRNATarget/

miRNA Interaction DB : http://starbase.sysu.edu.cn/

Sequencing based miRNA DB : http://mirgator.kobic.re.kr/

predicted A-to-I edited miRNA DB : http://microrna.osumc.edu/mireditar/

Animal, plant and virus miRNA DB : http://lemur.amu.edu.pl/share/php/mirnest/

Atlantic Salmon miRNAs DB : http://www.molgenv.com/ssa_mirnas_db_home.php

miRNA prediction on UTRs : http://genie.weizmann.ac.il/pubs/mir07/mir07_prediction.html

Idea of analysing miRNA Sequencing data :

http://www.illumina.com/applications/epigenetics/small_rna_analysis.ilmn

More:

http://www.bioconductor.org/help/search/index.html?q=miRNA+target

Alien Genome !!!

Jit — Sat, 13 Dec 2014 00:24:32 -0600

Genome sequencing, analysis and expression of Alien genome.

Note: This image/cartoon is create only for fun. It has nothing to do with any scientific findings.