BOL: Related items

World of Omics

Rahul Agarwal — Tue, 16 Jul 2013 17:11:48 -0500

How many variants of "omics" techniques presently in use ?

Should you get sequenced? Not all bad genes predict disease

Rahul Agarwal — Thu, 29 Aug 2013 15:10:53 -0500

“What we really don’t know yet is whether the predictive aspects of the genome are going to turn out to be beneficial or potentially harmful”

“As we roll out genomic medicine we are fighting against this society-wide misconception that having the bad gene means you’re going to get the disease. That’s only true in a very few cases.”

Source:Today Health

Address of the bookmark: http://www.today.com/health/should-you-get-sequenced-not-all-bad-genes-predict-disease-8C11017154

320000 viruses in mammals yet to sequenced in future!!!

Rahul Agarwal — Tue, 03 Sep 2013 08:35:30 -0500

With current biological technique improvements, finally it is now possible to look at millions of unknown viruses at genomic level and understand the mechanism. According to available data, close to 70 per cent of emerging viral diseases such as HIV/AIDS, West Nile, Ebola, SARS, and influenza, are zoonoses - infections of animals that cross into humans.

To address the challenges of describing and estimating virodiversity, a team of investigators from Center for Infection and Immunity (CII) and EcoHealth Alliance began in jungles of Bangladesh - home to the flying fox.

Reference:

http://economictimes.indiatimes.com/news/news-by-industry/et-cetera/mammals-harbour-at-least-320000-new-viruses/articleshow/22253268.cms

http://www.bbc.co.uk/news/science-environment-23932400

DNA tale of 3 to 4 years old Serbia boy

Rahul Agarwal — Tue, 26 Nov 2013 17:34:00 -0600

The genome of a young boy found underground at Mal’ta near Lake Baikal of eastern Siberia around 24,000 years ago came out as close relative of Europeans and Native Indians.

Link:

http://www.nytimes.com/2013/11/21/science/two-surprises-in-dna-of-boy-found-buried-in-siberia.html?_r=0

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12736.html

Genome of Rainbow Trout Sequenced

Rahul Agarwal — Fri, 25 Apr 2014 10:36:51 -0500

Major finding:

“In humans and most vertebrates the duplication events were older so there are fewer duplicated genes still present. Most of the duplicated genes get lost or modified so much that they are no longer recognizable as duplicates over time. In the trout and salmon we can see an earlier stage in the process and many duplicated genes are still present,” said Dr Gary Thorgaard of Washington State University, a co-author of the paper published in the journal Nature Communications.

Source:

http://www.sci-news.com/genetics/science-genome-rainbow-trout-01877.html

Real time Sequencing

Rahul Agarwal — Sun, 04 May 2014 18:16:42 -0500

“... we now know we can do high-throughput sequencing at any location on Earth,” Moroz said.

Source:

http://news.ufl.edu/2014/04/28/real-time-genome-sequencing-at-sea/

Drawback of Exome Sequencing

Rahul Agarwal — Mon, 02 Jun 2014 05:46:43 -0500

Dr Eric Londin, Assistant Professor, Thomas Jefferson University, USA, stated that analysis of 44 exome datasets from four different testing kits showed that they missed a high proportion of clinically relevant regions in the 56 ACMG genes. "At least one gene in each exome method was missing more than 40 percent of disease-causing genetic variants, and we found that the worst-performing method missed more than 90 percent of such variants in four of the 56 genes," he says.

Source: http://www.eurekalert.org/pub_releases/2014-05/esoh-pco052914.php

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.

LoRMA: a tool for correcting sequencing errors in long reads such those produced by Pacific Biosciences sequencing machines

Jit — Wed, 15 Jun 2016 17:18:36 -0500

LoRMA is a tool for correcting sequencing errors in long reads such those produced by Pacific Biosciences sequencing machines.

Publication:

L. Salmela, R. Walve, E. Rivals, and E. Ukkonen: Accurate selfcorrection of errors in long reads using de Bruijn graphs. Accepted to RECOMB-Seq 2016.

Download:

Address of the bookmark: https://www.cs.helsinki.fi/u/lmsalmel/LoRMA/

Grinder / Biogrinder - A versatile omics shotgun and amplicon sequencing read simulator

Jit — Wed, 24 May 2017 08:41:41 -0500

Grinder is a versatile program to create random shotgun and amplicon sequence libraries based on DNA, RNA or proteic reference sequences provided in a FASTA file.

Grinder can produce genomic, metagenomic, transcriptomic, metatranscriptomic, proteomic, metaproteomic shotgun and amplicon datasets from current sequencing technologies such as Sanger, 454, Illumina. These simulated datasets can be used to test the accuracy of bioinformatic tools under specific hypothesis, e.g. with or without sequencing errors, or with low or high community diversity. Grinder may also be used to help decide between alternative sequencing methods for a sequence-based project, e.g. should the library be paired-end or not, how many reads should be sequenced.

Address of the bookmark: https://sourceforge.net/projects/biogrinder/files/biogrinder/