BOL: Related items

Next generation sequencing(NGS) books

Abhimanyu Singh — Fri, 30 May 2014 04:48:04 -0500

Employing different technologies, the purpose of NGS platform is to decode the identity or modification on the nucleotides. NGS platforms evolve quickly and capture the main stream.

This bookmark is created to provide NGS online books links.

Address of the bookmark: http://en.wikibooks.org/wiki/Next_Generation_Sequencing_%28NGS%29/Print_version

Research Scientist – National Institute of Cholera and Enteric Diseases

Wed, 22 Oct 2014 10:26:46 -0500

The following post is to be filled up on purely temporary basis under the project entitled "Second phase of Task Force Biomedical Informatics Center of ICMR" under Dr. Santasabuj Das, Scientist 'D' of this Institute:-

01. Scientist II 01
Essential: Ph.D. degree in Life Sciences from a recognized university along with a minimum of 2 years of research experience in Bioinformatics as evidenced by publications in the peer reviewed journals.

OR
Ph.D. degree in Bioinformatics from a recognized university.

OR
M.Sc. in Bioinformatics from a recognized university along with a minimum of 3 years of research experience in Bioinformatics as evidenced by publications in the peer reviewed journals.

Desirable:
Thorough Knowledge about In silico genome analysis and comparative genomics.
Experience with in silico identification of novel virulence factors of pathogens, host-pathogen interactions and Systems Biology.
Additional Postdoctoral research experience in relevant subjects from a recognized institutions.

Rs. 44,000/- p.m. (consolidated) plus 30% HRA

Below 40 years

Applications along with Bio-Data containing detail work experience and full list of publications may be sent via email tosantasabujdas@yahoo.com latest by October 27, 2014.

Short-listed candidates will be called via email for an interview to be held at the institute in the second week of November, 2014.

Advertisement: www.niced.org.in/placements.htm

Will MinION Nanopore sequencing increase the number of Next Generation Sequencing projects?

Strand — Tue, 04 Aug 2015 05:14:07 -0500

Will MinION Nanopore sequencing increase the number of Next Generation Sequencing projects?

Celebrating Crystallography - An animated adventure

Fri, 31 Oct 2014 15:59:00 -0500

NEW: Now with French or Spanish subtitles (click on the 'Captions' icon to select). Plus... Watch the French language version here: https://www.youtube.com/watch?v=PvLu7BOsJhM X-ray crystallography is arguably one of the greatest innovations of the twentieth century, but not that many people know what it is or how it came about. Join us on an animated journey through the 100 year history of crystallography -- from the pioneering work of William and Lawrence Bragg in 1913 to the surface of Mars! Narrated by structural biologist Stephen Curry and produced by animation company 12foot6, the film explores the extraordinary history of crystallography. To date 28 Nobel Prizes have been awarded to projects related to the field and X-ray crystallography remains the foremost technique in determining the structures of a huge range of complex molecules. This film was produced in celebration of the Bragg Centenary and was funded by STFC. Watch more science videos on the amazing Ri Channel: http://richannel.org Watch more animations from 12foot6: http://12foot6.com/ The Ri is on Twitter: http://twitter.com/ri_science and Facebook: http://www.facebook.com/royalinstitution Subscribe for the latest science videos: http://richannel.org/newsletter

Finishing !!

Jit — Sat, 20 May 2017 15:50:20 -0500

The process of finishing a genome and moving it from a draft stage (the result of sequencing and initial assembly) to a complete genome is typically a time and resource intensive task. The advent of new sequencing technologies has come with its own set of opportunities and pitfalls in the finishing process. While genomes can now be sequenced to high redundancy in a cost-effective manner, the process of assembling the genomes is more challenging and often draft genomes are fragmented into hundreds of contigs. Correspondingly, the task of producing the complete genome can involve months of lab work and thousands of finishing experiments and is usually done in large genome centers.

The work in our lab has focussed on computational approaches to speed-up the finishing process. Specifically, we have explored the use of optical mapping and mate-pair data to augment assemblies and direct finishing experiments. The tools developed in our lab have been used in several finishing projects, producing complete genomes (and near-complete ones) with surprisingly little computational and experimental effort (Nagarajan et al., in submission). The executables (as well as source code) for these tools are freely available here:

Scaffolding using Optical Restriction Mapping
Optical Maps are global, ordered maps of restriction site locations in a genome. This information can be quite useful in scaffolding contigs from a shotgun assembly to guide the finishing process. A set of programs to exploit optical maps for assembly can be found here: SOMA v2.0 (63 MB tar.gz file). This version of SOMA contains several improvements to programs in v1.0 as well as new scripts for working with multiple maps, contig graphs and scaffolds.
Augmenting assemblies with mate-pair data
Mate-pair information can be valuable in augmenting short-read assemblies and reconstructing the genome as larger scaffolds. AMOS-Hybrid is a pipeline written in the AMOS framework (open-source assembly tools) to merge arbitrary mated reads into an existing assembly and merge contigs and create scaffolds where possible. Source code and executables for AMOS-Hybrid are available here: AMOS-Hybrid v1.0 (142 MB tar.gz file).
Assembly and sequence-composition guided finishing
Contigs from a shotgun assembly are typically linked together in a graph structure that can serve to guide finishing and in some case close gaps in-silico. Also, in many cases, sequence composition of contigs can provide clues to fill gaps in scaffolds. A set of scripts to automate some of these tasks can be found here: Finishing Scripts v1.0 (63 MB tar.gz file).

http://www.cbcb.umd.edu/finishing/

Address of the bookmark: http://www.cbcb.umd.edu/finishing/

Postdoctoral fellowship in Bioinformatics

Sat, 08 Nov 2014 14:41:14 -0600

A two-year post-doctoral position is available in the Biocomputing group of the Sapienza University led by Anna Tramontano to work on either genomics research or structural bioinformatics, focusing on the study of relevant biomedical problems.
The ideal candidate should be motivated and talented, hold a PhD degree, have good programming skills, a grasp of statistical methods and an understanding of biology.
Experience in the development of computational biology methods would be an added value.

Good communication skills and fluency in spoken and written English are required.
Please apply sending a curriculum vitae, the names of at least two referees and a letter of motivation describing past experience and future goals to anna.tramontano@uniroma1.it with subject: “Application for post-doctoral position November 2014 YOUR LAST NAME”

Deadline: No later than November 28th, 2014.
Duration: 2 years

Salary on grant: Commeasured to the experience of the candidate
Contact Person (Referent): Anna Tramontano
Ref. E-Mail: anna.tramontano@uniroma1.it
Group Web Page: http:/www.biocomputing.it

PLAST: A fast, accurate and NGS scalable bank-to-bank sequence similarity search tool

Jit — Fri, 01 Dec 2017 04:10:54 -0600

PLAST is a fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations of seeds-based heuristic comparison methods, such as the Blast suite of algorithms.

Relying on unique software architecture, PLAST takes full advantage of recent multi-core personal computers without requiring any additional hardware devices.

PLAST stands for Parallel Local Sequence Alignment Search Tool and is was published in BMC Bioinformatics.

PLAST is a general purpose sequence comparison tool providing the following benefits:

PLAST is a high-performance sequence comparison tool designed to compare two sets of sequences (query vs. reference),
Reduces the processing time of sequences comparisons while providing highest quality results,
Contains a fully integrated data filtering engine capable of selecting relevant hits with user-defined criteria (E-Value, identity, coverage, alignment length, etc.),
Does not require any additional hardware, since it is a software solution. It is easy to install, cost-effective, takes full advantage of multi-core processors and uses a small RAM footprint,
Ready to be used on desktop computer, cluster, cloud as well as within distributed system running Hadoop.

https://plast.inria.fr/

Address of the bookmark: https://plast.inria.fr/

Centre for Systems Biology & Bioinformatics, Panjab University vacancy of Research Fellow

Wed, 12 Nov 2014 06:18:54 -0600

Applications are invited along with complete bio-data and attested copies of certificates of qualifications, experience etc. for the one post of
Research Fellow and one post of Program Assistant under PURSE Grant of the University in Centre for Systems Biology & Bioinformatics, UIEAST, Panjab University, Chandigarh which is tenable till the period of the project

Essential Qualification
For Research Fellow:-
M.Sc. in Systems Biology and Bioinformatics / Life
Sciences with minimum 55% marks.
Preference will be given to NET/GATE/ICMR qualified candidates without fellowship however, candidates who have cleared the Panjab University Ph.D. entrance test in Systems Biology & Bioinformatics will also be eligible.

Applications should be reach on or before 19-11-2014 in the office of the undersigned. Interview will be held on 21-11-2014 in the office of the Coordinator, Centre for Systems Biology & Bioinformatics, South Campus, Block-3, Sector-25, Panjab University, Chandigarh. No TA/DA will be paid.

more at http://jobs.puchd.ac.in/includes/jobs/2014/20141110143634-Advertisement.pdf

Porechop: tool for finding and removing adapters from Oxford Nanopore reads

Rahul Nayak — Tue, 29 May 2018 07:33:44 -0500

Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments to effectively find adapters, even at low sequence identity.

Porechop also supports demultiplexing of Nanopore reads that were barcoded with the Native Barcoding Kit, PCR Barcoding Kit or Rapid Barcoding Kit.

Address of the bookmark: https://github.com/rrwick/Porechop

Bioinformatics JRF/RA/SRF position at Institute of Cytology and Preventive Oncology (ICPO)

Wed, 19 Nov 2014 20:16:32 -0600

Institute of Cytology and Preventive Oncology (ICPO) I-7, Sector-39, Noida-201301

Candidates having the below mentioned qualifications may appear for walk in interview at ICPO on 2nd December 2014 between 10.00 AM and 12:00 PM under the below time bound projects under Dr. Subhash M. Agarwal, Scientist C. The post is purely temporary and co-terminus with the project.

Research Assistant (One)
25650/- consolidated
Discovery of EGFR secondary mutant inhibitors using structure based screening approach (ICMR)
Duration: 7 months

Essential: M.Sc./ M.Tech in Bioinformatics or any other related subject with good academic record.

Desirable: Experience in scripting and molecular docking.

Below 30 years

Junior Research Fellow (One)

16,000 + 30% HRA = Rs. 20800/-

Identification of novel inhibitors targeting EGFR using an integrated ligand and structure based approach (DBT)

Duration: 9 months

Essential: M.Sc./ M.Tech in Bioinformatics or any other related subject with good academic record. Candidates with CSIR-UGC / ICMR, NET qualification will be preferred

Desirable: Experience in scripting, QSAR and molecular docking.

Below 28 years

Interested eligible candidates may send their applications with Bio-data by email at (smagarwal@gmail.com) or by post addressed to Dr. Subhash M Agarwal, Scientist C, Institute of Cytology and Preventive Oncology (ICPO) I-7, Sector-39, Noida-201301 so as to reach latest by 1st December, 2014. The candidates may appear for interview at ICPO along with 3 copies of CV, photo and relevant certificates of qualifications in original and reprints of publications at the time of interview. It should be noted that No TA/DA will be paid for the walk in Interview.