BOL: Related items

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/

RECRUITMENT FOR 6 POSITIONS OF JRF (Junior Research Fellow)

Thu, 04 Jun 2015 15:22:54 -0500

Institute of Bioresources and Sustainable Development (IBSD), a National Institute of the Department of Biotechnology, Government of India invites applications for 6 positions of JRF for 2015. The main mandate of IBSD is Conservation and Sustainable Utilization of Bioresources for the Socio-economic Development of the North East Region of India, which is a genetic treasure trove of plants, animals and microbial resources. This region falls among the World’s top 10 Biodiversity Hotspots. The broad areas of research are in Plant Bioresources, Microbial Resources, Natural Product Chemistry, Animal Bioresources and Bioinformatics and Database Management.

Minimum qualifications: M.Sc. with minimum 55% for general and OBD Category (55% for SC/St/PH) in the above-mentioned subject areas (viz. Biotechnology, Life Sciences, Microbiology, Botany, Plant Sciences, Chemistry, Zoology, Animal Sciences, Fishery Sciences and any other relevant branches).

Preference will be given to those holding valid CSIR-UGC NET JRF. DBT-JRF, ICAR-JRF, ICMR-JRF and DST-INSPIRE Fellowship while NET/SLET/SET qualified and GATE qualified candidates (90 or above percentile) are also encouraged to apply. Reservations of seats: 15% for SC, 7.5% for ST, 27% for OBC (noncreamy layer) and 3% for Physically Handicapped as per statutory norms.

Selection Procedure: If the number of JRF and INSPIRE qualified candidates is more, selection will be based on interview of the JRF and INSPIRE qualified candidates only. The selected candidates may be registered for Ph.D. in any of the recognized Universities in India.

Application Procedure: Application should be sent in the prescribed application form (available on the IBSD website). The candidate should send the completed and signed form along with self attested copies of all supporting certificates and marksheets along with an application fee of Rs.300/- (For GEN/OBC/PH) & Rs.150/- for (SC/ST), for which a Demand Draft in favour of ‘Institute of Bioresources and Sustainable Development, payable at Imphal, Manipur, should be attached with the application form. Candidates are advised to provide their email ID and mobile number as they would be contacted electronically by the Institute. Duly filled applications (with ‘Application for IBSD PhD Programme’ super scribed on the envelope) should be sent to ‘The Director, Institute of Bioresources and Sustainable Development, Takyelpat, Imphal-795001, Manipur so as to reach on or before 6th of July, 2015. Applications send by email with scan copy of required enclosures will also be accepted and can be sent to director.ibsd@nic.in. However, in such instances, the application will be processed only after the receipt of the mailed hard copies.

Advertisement: http://ibsd.gov.in/jobs/phd_2015/IBSD_JRF_2015.pdf

Application Form : http://ibsd.gov.in/jobs/phd_2015/APPLICATION_FORM.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

Rosalind Problem Solution with Perl

Jit — Tue, 09 Jun 2015 23:35:18 -0500

Rosalind is a platform for learning bioinformatics and programming through problem solving. Take a tour to get the hang of how Rosalind works.

Bioinformatics Textbook Track

Find more about Rosalind puzzle at http://rosalind.info/problems/list-view/?location=bioinformatics-textbook-track

I will provide solution of all the Rosalind problem with Perl for community.

Check out the right sidebar for more links ...

RNA-seq Analysis Workshop Course Materials

Jit — Tue, 03 Jul 2018 08:14:14 -0500

RNAseq can be roughly divided into two "types": Reference genome-based - an assembled genome exists for a species for which an RNAseq experiment is performed. It allows reads to be aligned against the reference genome and significantly improves our ability to reconstruct transcripts. This category would obviously include humans and most model organisms but excludes the majority of truly biologically intereting species (e.g., Hyacinth macaw); Reference genome-free - no genome assembly for the species of interest is available. In this case one would need to assemble the reads into transcripts using de novo approaches. This type of RNAseq is as much of an art as well as science because assembly is heavily parameter-dependent and difficult to do well. In this lesson we will focus on the Reference genome-based type of RNA seq. http://chagall.med.cornell.edu/RNASEQcourse/

Address of the bookmark: http://chagall.med.cornell.edu/RNASEQcourse/

Research Associate MANIT - Allahabad, Uttar Pradesh

Fri, 12 Jun 2015 05:44:38 -0500

Applications are invited from Indian nationals for the post of Research Assistant (on contract) in research project entitled “Identification of novel drug targets in Aspergillus fumigatus genome prioritized by essentiality based screening and rational designing of new antifungal compounds” sanction order no. CST/238 dated 12/05/2015 sponsored by Council of Science and Technology U.P.

The duly completed application on prescribed format along with copies of supporting documents must reach to: Office of the Dean (Research & Consultancy), Motilal Nehru National Institute of Technology, Allahabad-211004 on or before 03/07/2015.

The position is purely temporary and will be governed by the funding agency rules & service conditions of Office of the Dean (Research & Consultancy), MNNIT Allahabad.

For detail advertisement see: www.mnnit.ac.in/images/newstories/Advertisement_for_the_post_of_Research_Assistant_in_UPCST_Project_of_Biotechnology_Department.pdf

AlignQC: A tool for assessing an alignment, and generating reports that are easy to share

Jit — Tue, 07 Aug 2018 04:41:07 -0500

Long read alignment analysis. Generate a reports on sequence alignments for mappability vs read sizes, error patterns, annotations and rarefraction curve analysis. The most basic analysis only requires a BAM file, and outputs a web browser compatible xhtml to visualize/share/store/extract analysis results.

https://f1000research.com/articles/6-100/

https://github.com/jason-weirather/AlignQC

Address of the bookmark: https://www.healthcare.uiowa.edu/labs/au/AlignQC/

Research Associate at International Centre for Genetic Engineering and Biotechnology (ICGEB)

Wed, 17 Jun 2015 18:49:05 -0500

Research Associate
International Centre for Genetic Engineering and Biotechnology (ICGEB)
Address: Aruna Asaf Ali Marg, Jawaharlal Nehru University, New Delhi
Postal Code: 110067
City: New Delhi
State: Delhi
Qualifications: Experience in many docking softwares and operating systems is essential. Additional experience in bioinformatics and computational biology tools will be useful.
Details will be available at: http://www.icgeb.org/vacancies.html

How To Apply: Submit curriculum vitae to: sb.icgeb@gmail.com
Last Date: 5 July 2015

Platypus: A Haplotype-Based Variant Caller For Next Generation Sequence Data

Shruti Paniwala — Thu, 25 Oct 2018 06:14:55 -0500

Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data. By using local realignment of reads and local assembly it achieves both high sensitivity and high specificity. Platypus can detect SNPs, MNPs, short indels, replacements and (using the assembly option) deletions up to several kb. It has been extensively tested on whole-genome, exon-capture, and targeted capture data, it has been run on very large datasets as part of the Thousand Genomes and WGS500 projects, and is being used in clinical sequencing trials in the Mainstreaming Cancer Genetics programme.

Tutorial https://github.com/andyrimmer/Platypus/blob/master/misc/README.txt

Address of the bookmark: http://www.well.ox.ac.uk/platypus

Research Associate Bioinformatics job position in Indian Agricultural Statistics Research Institute (IASRI), Pusa, New Delhi

Wed, 17 Jun 2015 20:48:40 -0500

Research Associate Statistics

Eligibility : M Phil / Phd, MSc

Location : Delhi

Last Date : 27 Jun 2015

Hiring Process : Walk - In
Indian Agricultural Statistics Research Institute (IASRI) - Job DetailsDate of posting:03 Jun 15

Research Associate Statisticsjob position in Indian Agricultural Statistics Research Institute (IASRI)
on purely contractual temporary basis

Project : “ICAR-Network Project of Transgenic in Crops”

Qualification : Ph.D. in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application/ Life Science/ Biotechnology/ Agricultural Science or equivalent OR Post-Graduation in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application/ Life Science/ Biotechnology/ Agricultural Science or equivalent with 1st Division or 60% marks or equivalent with at least two years of research experience.

No.of Post: 01

Emoluments for RA: Consolidated Rs. 24000/- per month + 30% HRA for Ph.D holders and consolidated Rs. 23000/- per month + 30% HRA for Master Degree.

Age Limit : 40 years
How to apply

Walk-in-interview will be held on 27th June 2015, 10.30 A.M at IASRI, Pusa, New Delhi

More at http://iasri.res.in/employment/employment.htm