BOL: Related items

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

Bioinformatics Algorithms (Part 1) with Pavel Pevzner, Phillip E. C. Compeau,

Mon, 30 Sep 2013 11:34:09 -0500

The course Bioinformatics Algorithms (Part 1) by Pavel Pevzner, Phillip E. C. Compeau, and Nikolay Vyahhi from University of California, San Diego will be offered free of charge to everyone on the Coursera platform. Sign up at http://www.coursera.org/course/bioinformatics.

Walk-in-Interview @ Indian Agricultural Statistics Research Institute

Wed, 02 Oct 2013 15:40:17 -0500

Indian Agricultural Statistics Research Institute
Library Avenue, Pusa, New Delhi – 110012

Walk-in-Interview

Walk-in-interview will be held on October 5, 2013 at 10:00 A.M. at IASRI, New Delhi for a project “A New Distributed Computing Framework for Data Mining” funded by Department of Electronics and Information Technology, Government of India for the following posts. The appointment will be on contractual basis upto 14th October, 2015 or till the termination of the project whichever is earlier and the incumbent shall not have any claim for regular appointment under ICAR.

Research Associate

Ph.D. in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application or equivalent or

Post-Graduation in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application or equivalent with 1st Division and at least two years of research experience

 Knowledge of Statistical Analysis /Bioinformatics tools for computational genomics.

 Knowledge of R/Perl programming language

Research Associate

Ph.D. in Computer Science/ Computer Application / Bioinformatics/ Agricultural
Statistics/ Statistics or equivalent or

Post-Graduation in Computer Science/ Computer Application /Bioinformatics/ Agricultural Statistics/ Statistics or equivalent with 1st Division and at least two years of research experience

 Expertise in Java programming.
 Knowledge of system administration and networking under Linux environment.
 Knowledge of parallel programming and cluster computing.

Emoluments for Research Associate: Consolidated Rs:24000/- per month + HRA (for Ph.D. Degree holders) and Rs:23000/- per month + HRA (for Master’s Degree holders)

Age Limit: Age should be not more than 40 years (5 years relaxation for SC/ST/women candidates and 3 years for OBC candidates as on date of interview).

Interested candidates are requested to appear for Walk-in-Interview on the date and time as specified above in Room No. 106, Training Cum Administrative Block of the Institute along with their application giving bio-data with attested copies of certificates, degrees, testimonials, etc. and one passport size photograph.

Original certificates/ Degrees are needed to be produced at the time of interview.

No T.A. /D.A. will be paid for appearing in the interview.

Advertisement: http://www.iasri.res.in/employment/employment.htm

How DNA is Packaged (Advanced)

Mon, 23 Sep 2013 18:08:34 -0500

Each chromosome consists of one continuous thread-like molecule of DNA coiled tightly around proteins, and contains a portion of the 6,400,000,000 basepairs (DNA building blocks) that make up your DNA. Originally created for DNA Interactive ( http://www.dnai.org ). TRANSCRIPT: In this animation we'll see the remarkable way our DNA is tightly packed up to fit into the nucleus of every cell. The process starts with assembly of a nucleosome, which is formed when eight separate histone protein subunits attach to the DNA molecule. The combined tight loop of DNA and protein is the nucleosome. Six nucleosomes are coiled together and these then stack on top of each other. The end result is a fiber of packed nucleosomes known as chromatin. This structure, is then looped and further packaged using other proteins (which are not shown here) to give the final "chromosomal" shapes. It is this remarkable multiple folding which allows six feet of DNA to fit into the nucleus of each cell in our body. And a typical cell nucleus is so small that ten thousand could fit on the tip of a needle. It is important to realize that chromosomes are not always present, they form only when cells are dividing. At other times, as we can see here at the end of cell division, our DNA becomes less highly organized.)

Shendure Lab

Wed, 09 Oct 2013 14:21:58 -0500

The Shendure Lab is part of the Department of Genome Sciences at the University of Washington (Seattle, WA). The mission of the lab is to develop and apply new technologies in genomics and molecular biology. Most projects in the lab exploit new DNA sequencing technologies (Shendure et al., Nature Reviews Genetics 2004; Shendure & Ji, Nature Biotechnology 2008; Shendure & Lieberman Aiden, Nature Biotechnology 2012), and generally fall into one of six areas: 1) next-generation human genetics; 2) genome contiguity & completeness; 3) massively parallel functional analysis; 4) molecular tagging; 5) synthetic biology; 6) translational genomics. Our interests in each of these areas are outlined briefly below, and a full list of publications is available via PubMed. http://www.ncbi.nlm.nih.gov/pubmed?cmd=search&term=shendure
More http://krishna.gs.washington.edu/research.html

Lab page @ http://krishna.gs.washington.edu/index.html

Nucl2Vec: Local alignment of DNA sequences using Distributed Vector Representation

Jit — Tue, 16 Mar 2021 05:45:44 -0500

We demonstrate a novel approach forlocal alignment of DNA reads with respect to reference genome.For this process we have used Skip-gram model for creatingencoding(Nucl2Vec) and k-nearest neighbor for the alignment.With our new approach we have reduced computation cost forlocal alignment , while achieving accuracy comparable to existingdefacto standard BWA-MEM tool.

https://prakharg24.github.io/papers/401851.full.pdf

Address of the bookmark: https://prakharg24.github.io/papers/401851.full.pdf

Shankar Lab

Wed, 16 Oct 2013 07:02:22 -0500

Research Interest:

(A) Regulatory System Analysis with respect to microRNAs

(B) Computational Epigenomics & Regulomics:

Department of Biotechnology,
Institute of Himalyan Bioresources Technology
CSIR, Palampur(Himachal Pradesh), India.
Email: ravishihbt.res.in; ravish9gmail.com

More @ http://scbb.ihbt.res.in/SCBB_dept/Lab_Member.php

SLIDESORT-BPR

Abhimanyu Singh — Mon, 20 Nov 2017 09:19:52 -0600

Chromosomal rearrangement events are caused by abnormal breaking and rejoining of DNA molecules. They are responsible for many of the cancer related diseases. Detecting the DNA breaking and repairing mechanism, therefore, may offer vital clues about the pathologic causes and diagnostic/therapeutic target of these diseases. But this effort also poses considerable challenges, because the structural variations and the genomes are different from one person to another. Intermediate comparison via reference genome could lead to the loss information. Unlike the current methods which make use the reference genome, we developed a method to detect the breakpoint reads directly from observing the differences between two (or more) NGS short reads samples. Slidesort-BPR is a command line tool implemented in C++.

Address of the bookmark: https://github.com/ewijaya/slidesort-bpr

DbBrowser: Attwood Lab

Fri, 18 Oct 2013 10:48:19 -0500

DbBrowser: Attwood Lab research concerns protein sequence analysis, primarily using the method of protein 'fingerprinting'. DbBrowser: Attwood Lab maintain a diagnostic fingerprint database (PRINTS), one of the founding partner of InterPro. We also design software to display sequence and structural data in visually-striking ways (e.g., Ambrosia, CINEMA); DbBrowser: Attwood Lab are building re-usable software components to create semantically integrated bioinformatics applications through UTOPIA, including a 'smart' PDF reader that links bioinformatics databases and tools directly with scientific articles (Utopia Documents); and have developed a number of tools for automatic annotation and text mining (e.g., MINOTAUR, PRECIS, METIS).

More @ http://www.bioinf.manchester.ac.uk/dbbrowser/index.php

Ra assembler - a de novo DNA assembler for third generation sequencing data

biogeek — Wed, 27 Dec 2017 20:36:54 -0600

Integration of the Ra assembler - a de novo DNA assembler for third generation sequencing data developed on Faculty of Electrical Engineering and Computing (FER), Ruder Boskovic Institute (RBI) and Genome Institute of Singapore (GIS).

Ra is in development since 2014 in the form of several separate components that used to be run individually.
This project aims to ease the usage of Ra by integrating it into a complete de novo assembly tool.

Unlike other state-of-the-art assemblers, Ra does not have an error correction step. Instead, it relies on detecting overlaps using a very sensitive and specific overlapper ("graphmap -w owler", https://github.com/isovic/graphmap) and constructing and reducing an overlap graph (Ra layout, https://github.com/mariokostelac/ra).

Address of the bookmark: https://github.com/mariokostelac/ra-integrate/