BOL: Related items

Bioinformatics approach to Boar Taint

Rahul Agarwal — Wed, 17 Jul 2013 15:50:37 -0500

Meat products obtained from intact male pigs often produce offensive smell or odour which is recognized as a complex genetic trait called boar taint.Androstenone and Skatole in the fat primarily cause boar taint. Metabolism of androstenone and sex steroids share a common pathway which makes removal of boar taint a very challenging task. Castration is a traditional solution to remove boar taint but it also results in bad quality of meat due to low level of steroids which is objectionable to many consumers. Detected functional variant(s) underlying boar taint compounds can be used as genetic markers in selection of male pigs with reduced boar taint levels. Resequencing of a total of 47 samples belong to Norwegian Landrace (NL) and Duroc (D) pigs with varied boar taint levels were done in Illumina HiSeq2000 to >10X average coverage. Short reads generated from these samples mapped to Sus Scrofa version 10.2 reference assembly using Bowtie2. Alignment file then used for calling SNPs and InDels inside previousy identified QTL regions on SSC5,13, and 7 with the aid of FreeBayes , a variant caller tool. A final list of SNPs was prepared after filtering SNPs on the basis of SNP quality, coverage of SNP allele, functional and structural annotation, and repeats, etc. Selected SNPs will be genotyped in sample population for validation and then used for constructing SNPs haplotypes in close linkage disequilibrium with QTLs and fine mapping of QTLs through association mapping of genotyped SNPs.

NGS Online Training

Sat, 27 Sep 2014 07:42:29 -0500

ArrayGen Technologies announces to provide online NGS training through out the globe. Now analyze your own NGS datasets from anywhere.For more information contact us at training@arraygen.com

Please visit our site at www.arraygen.com

Want to Know which genome assembler rule the world ?

Rahul Agarwal — Sun, 11 Aug 2013 11:42:32 -0500

Assemblathon 2: evaluating de novo methods of genome assembly

http://www.gigasciencejournal.com/content/2/1/10/abstract

http://blogs.nature.com/news/2013/07/genome-assembly-contest-prompts-soul-searching.html

http://assemblathon.org/post/44431915644/feedback-and-analysis-of-the-assemblathon-2-p

JRF in Bioinformatics @ INMAS, DRDO,Delhi

Wed, 01 Oct 2014 07:01:07 -0500

Institute of Nuclear Medicine and Allied Sciences (INMAS), Delhi under the aegis of Defence Research and Development Organisation (DRDO), is engaged in research and developmental work in radiation sciences, Neuro-Computing and Medical Image Processing. INMAS is looking for meritorious young researchers for pursuing research in the frontier areas at INMAS. The Institute invites applications from young and meritorious Indian nationals who are creative, have passion and desire to pursue R&D in frontier areas. INMAS possesses ambience of a research cum academic institute coupled with an advanced R&D infrastructure in a mission mode. It provides the best infrastructure, motivation and personality development prospects for talented students, dreaming of unparalleled success in their professional endeavors. INMAS provides state of the art research facilities for undertaking pioneering research with defence applications.

JRF (Maximum Tenure‐ Five Years: 2yrs as JRF and 3yrs as SRF)
A first class Master’s Degree in Bioinformatics (likely 2 posts)
Around Rs 16,000/ Plus 30% HRA (as per rules of funding agency)

Applications are invited from candidates possessing the above qualifications. The upper age limit is as on the last date for receipt of application. (5 years relaxation to SC/ST candidates, 3 years to OBC candidates, and other entitled categories as per Govt rules). Actual No. of vacancies may vary.

Application form can be download from the website www.drdo.gov.in and E Mailed to inmashrd@gmail.com.
Last date to apply by email is 1700 hrs on 15 Oct 2014
Incomplete applications are liable to be rejected.
Confirmation will be sent to short-listed candidates through email only
Antecedents of selected candidates will be verified.
Written Test will be conducted from 0930-1030 hrs. Latecomers will not be considered.
Candidates will be required to produce certificates/testimonials in original at the time of interview.
It may please be noted that offer of Fellowship does not confer on fellows any right for absorption in DRDO.
Candidates should carry photocopy of Application form sent by email with them.
No TA/DA will be paid for attending interview & on joining.
Last date to apply by email is 1700 hrs on 15 Oct 2014

More at http://drdo.gov.in/drdo/English/jrf29092014.pdf
http://drdo.gov.in/drdo/English/index.jsp?pg=inmas29092014.jsp

Barber pole worm , sheep pathogen sequenced !!!

Rahul Agarwal — Tue, 03 Sep 2013 16:32:18 -0500

Haemonchus contortus is a highly pathogenic parasitic nematode of that can infect a large number of wild and domesticated ruminant species and is the most economically important parasite of sheep and goats worldwide. Scientists at the Wellcome Trust Sanger Institute have sequenced the genome of the barber's pole worm (Haemonchus contortus), which will help to explore the this tropical parasite which been disseminated around the world by livestock movement.

H. contortus is a member of the superfamily trichostrongyloidea (Strongylida) which contains most of the economically important parasitic nematodes of grazing livestock. These parasites cost the global livestock industry billions of dollars per annum in lost production and drug costs. A common type of clover may be a preventative or palliative for the disease. However, some particular breeds of sheep, such as the Gulf Coast Native from the Southern United States, have been shown to have developed special resistance to H. contortus.

Getting the full genome can help to tackle the problem and understand the resistance mechanism with an ease. Moreover, the genome could now provide a comprehensive understanding of how treatments against parasitic worms work and point to further new treatments and vaccines. By comparing the genome of the barber's pole worm with those of worms that have acquired drug resistance, researchers expect to reveal information about how and why resistance has occurred. Till now, researchers have uncovered essential information in the fight against drug resistance in worms.

Reference:

http://www.fwi.co.uk/articles/28/08/2013/140758/researchers-close-in-on-worm-resistance-in-sheep.htm

http://www.sciencedaily.com/releases/2013/08/130828103351.htm?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+sciencedaily%2Fplants_animals+(ScienceDaily%3A+Plants+%26+Animals+News)

Image source: Wikipedia

Internship Program for Bioinformatics / Biotechnology Professionals (No. Of Vacancy: 2)

Wed, 08 Oct 2014 01:10:08 -0500

ArrayGen is offering an Internship Program for Post graduate Bioinformatics / Biotechnology students and professionals. ArrayGen Technologies provide an excellent opportunity to gain research experience and explore if a scientific career is right for you. Currently we offer positions to outstanding students interested in Next Generation Sequencing (NGS) data analysis. Applications are accepted throughout the year. Accepted students will be listed on web with their schedules. Accepted students can attend our future workshops and trainings freely at the specified venue.

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/

How far can bioinformatics go creating organisms used for testing?

Fri, 17 Oct 2014 02:08:16 -0500

"I think you can get very far on a technical level. The problem is that a human body is more complex than just one cell." ... "At some point we still need clinical tests on animals and humans before we use it for real treatment. But we will likely be able to remove 99 % of animal tests in the future." Erik Lindahl, Professor of Theoretical and Computational Biophysics at KTH Royal Institute of Technology is telling us about his work. From the episode "Science for life – mapping the building blocks of the human body". Watch the rest of the talk, and other talks at www.crosstalks.tv Crosstalks is an academic talkshow produced by KTH Royal Institute of Technology and Stockholm University.

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

Graduate research assistantships @ University of Nebraska-Lincoln (UNL)

Wed, 22 Oct 2014 10:05:31 -0500

Graduate research assistantships in quantitative genetics are available with Gota Morota in the Department of Animal Science at the University of Nebraska-Lincoln (UNL).

Current projects in the Morota lab include developing kernel-based whole-genome prediction and kernel-based genome-wide association models, polygenic modeling of binary traits, reexamining the results from quantitative genetics analysis in light of functional annotation, and extending kernel methods (such as GBLUP and RKHS) specifically tailored for diverse types of emerging omics data.

In addition, candidates will be expected to leverage opportunities to interact with faculty in animal genetics and biometrics at the UNL in the areas of bioinformatics, breeding, functional genomics, quantitative genetics, and molecular genetics.

Candidates should have a B.S. or M.S. degree in quantitative disciplines with strong background and interest in statistical computing.
The starting date is Fall 2015.
For more information about research in the Morota lab at the UNL, visit: http://www.morotalab.org

A letter of interest in the position, C.V., and contact information for
three references should be emailed to Gota Morota at .
Review of applications will begin immediately, and continue until the
positions are filled. Informal inquiries are also welcome.

Also, please see: http://animalscience.unl.edu/anscprospectivegraduatestudents