BOL: Related items

Synima: Synteny Imaging tool

Jit — Sun, 10 Dec 2017 17:03:48 -0600

Synteny Imaging tool (Synima) written in Perl, which uses the graphical features of R. Synima takes orthologues computed from reciprocal best BLAST hits or OrthoMCL, and DAGchainer, and outputs an overview of genome-wide synteny in PDF. Each of these programs are included with the Synima package, and a pipeline for their use. Synima has a range of graphical parameters including size, colours, order, and labels, which are specified in a config file generated by the first run of Synima – and can be subsequently edited. Synima runs quickly on a command line to generate informative and publication quality figures. Synima is open source and freely available from https://github.com/rhysf/Synima under the MIT License.

Address of the bookmark: https://github.com/rhysf/Synima

AGRICUL AGRICULTURAL SCIENTISTS RECRUITMENT BOARD TURAL SCIENTISTS RECRUITMENT BOARD NEW DELHI-110 012

Wed, 11 Mar 2015 09:18:37 -0500

ADVERTISEMENT NO. 01/2015

PRINCIPAL SCIENTIST Pay Band: Minimum pay of `43,000 in the PB-4 of `37400-67000/- + RGP of `10,000/-.

Age: The candidates must not have attained the age of 52 years as on 24.03.2015. There shall be no age limit for the Council’s employees.

ICAR-NATIONAL INSTITUTE OF BIOTIC STRESS MANAGEMENT, RAIPUR (CHHATTISGARH)

57. Principal Scientist (Agricultural Entomology) (Two post)

Qualifications Essential:

(i) Doctoral degree in Agricultural Entomology including relevant basic sciences.

(ii) 10 years experience in the relevant subject out of which at least 8 years should be as Scientist/ Lecturer/Extension Specialist or in an equivalent position in the Pay Band- 3 of `15600-39100 with Grade Pay of `5400/`6000/`7000/`8000 and 2 years as a Senior Scientist or in an equivalent position in the Pay Band- 4 of ` 37400-67000 with Grade Pay of ` 8700/ ` 9000.

(iii) The candidate should have made contribution to research/teaching/extension education as evidenced by published work/innovations and impact.

Desirable:

(i) Experience of using frontiers research tools in management of insect pests of crop plants.

(ii) Evidence of contributions to relevant field through publications/ patents/citation index to suggest a vision/perspective in biotic stress research.

61. Principal Scientist (Bioinformatics) (One post)

Qualifications Essential:

(i) Doctoral degree in Bioinformatics including relevant basic sciences. (ii) & (iii) As in item no. 57 above.

Desirable:

(i) Experience of using bioinformatics for advancement of knowledge and for research on biotic stress management.

(ii) Evidence of contributions to relevant field through publications/patents/citation index to suggest a vision/perspective in biotic stress research.

http://asrb.org.in/administrator/uploads_dir/1424859407english.pdf

Multi-CAR: a tool of contig scaffolding using multiple references

Rahul Nayak — Tue, 06 Mar 2018 16:39:41 -0600

we design a simple heuristic method to further revise our single reference-based scaffolding tool CAR into a new one called Multi-CAR such that it can utilize multiple complete genomes of related organisms as references to more accurately order and orient the contigs of a draft genome. In practical usage, our Multi-CAR does not require prior knowledge concerning phylogenetic relationships among the draft and reference genomes and libraries of paired-end reads. To validate Multi-CAR, we have tested it on a real dataset composed of several prokaryotic genomes and also compared its accuracy performance with other multiple reference-based scaffolding tools Ragout and MeDuSa.

Address of the bookmark: http://genome.cs.nthu.edu.tw/Multi-CAR/

Research Associate at National Research Centre on Plant Biotechnology New Delhi

Mon, 16 Mar 2015 03:22:26 -0500

Walk-in interview will be held on 24-03-2015 at 10:00 AM at NRCPB, New Delhi for filling Research Associate and Senior Research Fellow positions as mentioned below. The positions are temporary and are initially offered for a period of one year. Details such as emoluments, qualifications, application format etc., are given below. Desirous candidates should report for interview latest by 10:30 AM with the application in the prescribed format, copies and originals of certificates, thesis and documents. No TA/DA will be provided for attending the interview.

ICAR-NPTC: Fibre development in flax/linseed.

(Job # 1) Research Associate (one) (Bioinformatics)

Rs.24000+ 30% HRA) for Ph.D. and for M. Sc Rs.23000/‐ (+ 30% HRA)

Ph.D. Degree in Bioinformatics/Molecular Biology/Biotechnology/ Genetics/allied sciences; or M. Sc in Bioinformatics/ Biotechnology/Life Sciences/ allied sciences with 1st division or 60% marks or equivalent overall grade point average with at least two years of research experience as evidenced from Fellowship/ Associate ship. 2 years research experience in bioinformatic data analysis/molecular biology techniques, and high throughput DNA/RNA sequencing, and transcriptome data analysis. Research paper with IF>1 will be desirable

ICAR-NPTC: Shade avoidance/low-light tolerance in rice.

General Terms & Conditions applicable to all the positions:
Age Limit: 35 years max. (5 years relaxation for SC/ST/OBC and woman candidates as per ICAR rules).
The positions are purely temporary, on a contractual basis and are initially offered for one year.
Originals must be shown for verification. 7. Research experience (Experience certificate from previous employer to be attached): I hereby declare that the information provided above is true to the best of my knowledge. Date: Signature

www.nrcpb.org/sites/default/files/ICAR-NPTC%20DBT%20RA%20SRF%20interview%2024th%20March.pdf

minialign: fast and accurate alignment tool for PacBio and Nanopore long reads

Jit — Thu, 24 May 2018 08:33:26 -0500

Minialign is a little bit fast and moderately accurate nucleotide sequence alignment tool designed for PacBio and Nanopore long reads. It is built on three key algorithms, minimizer-based index of the minimap overlapper, array-based seed chaining, and SIMD-parallel Smith-Waterman-Gotoh extension.

Address of the bookmark: https://github.com/ocxtal/minialign

Postdoctoral Fellowship in Bioinformatics and Evolutionary Genomics

Wed, 01 Apr 2015 21:36:42 -0500

Postdoctoral Fellowship in Bioinformatics and Evolutionary Genomics
Organization
National Human Genome Research Institute, National Institutes of Health
http://genome.gov/Staff/Baxevanis
Job Location
Bethesda, MD
Job Description

A postdoctoral training position is currently available in the Computational and Statistical Genomics Branch (CSGB) of the National Human Genome Research Institute (NHGRI). The position is located in the laboratory of Andy Baxevanis, Ph.D., whose research group uses comparative genomics approaches to better-understand the molecular innovations that drove the surge of diversity in early animal evolution. The overarching theme of Dr. Baxevanis’ research program is focused on how non-traditional animal models convey critical insights into human disease research.

Candidates should have or be close to obtaining a Ph.D. or equivalent degree in bioinformatics, computational biology, computer science, molecular biology, or a closely related field. Candidates with a background in evolutionary biology are particularly encouraged to apply. Programming skills and experience in the application of computational methods to genomic data are highly desirable. Applicants must possess good communication skills and be fluent in both spoken and written English. The ability to learn how to use new software and quickly become expert in its use, critical thinking, problem-solving abilities, and the ability to work semi-independently are required.
How to Apply

Interested applicants should submit a curriculum vitae, a detailed letter of interest, and the names of three potential referees to Dr. Baxevanis at andy@mail.nih.gov.
About Our Organization

The NIH Intramural Research Program is on the Bethesda, Maryland campus and offers a wide array of training opportunities for scientists early in their careers. The funding for this position is stable and offers the trainee wide latitude in the design and pursuit of their research project. The successful candidate will have access to NHGRI’s established and robust bioinformatics infrastructure, as well as resources made available through NIH’s Center for Information Technology (CIT) and the National Center for Biotechnology Information (NCBI).

For more information on CSGB and NHGRI’s Intramural Research Program, please see http://genome.gov/DIR/.

HiGlass: a tool for exploring genomic contact matrices and tracks.

Jit — Mon, 11 Jun 2018 09:44:49 -0500

HiGlass is a tool for exploring genomic contact matrices and tracks. Please take a look at the examples and documentation for a description of the ways that it can be configured to explore and compare contact matrices. To load private data, HiGlass can be run locally within a Docker container. The HiC data in the examples below is from Rao et al. (2014) http://higlass.io/

Address of the bookmark: http://higlass.io/

RA Bioinformatics at Bose Institute

Tue, 07 Apr 2015 03:30:25 -0500

Bose Institute, Kolkata, invites online applications from Indian Citizens for recruitment of Research Associate (05 posts) under Institute Plan Programmes : Improvement of Plants : Biotechnological, Genomic and Proteomic Approaches (programme No. – I), Bioinformatics and Computational Biology (programme No. – III), Microbial Genomics and Infection Biology (programme No. – V) and Basic & Applied Problems in Physical and Environmental Sciences (programme No. – VII). All the posts are tenable for one (01) year.

ESSENTIAL QUALIFICATION: PH.D. DEGREE IN LIFE SCIENCES / PHYSICAL SCIENCE.

Research Associate for Programme No. –I Specialization in the area of plant molecular biology or plant proteomic study or plant pathogen interaction.
Research Associate for Programme No. –I Specialization in the area of plant / fungal Biotechnology, tissue culture and molecular biology
Research Associate for Programme No. –III Specialization in the area of structural biology and protein crystallography.
Research Associate for Programme No. – V Specialization in the area of microbial physiology (metabolism) or environmental microbiology, with experience in microbial genomics and proteomics.
Research Associate for Programme No. – VII Specialization in the area of Theoretical High Energy Astrophysics or Astroparticle Physics. Proven record of independent research experience in Astrophysical
Radiation Magnetohydrodynamics or Cosmic Ray Astrophysics. Experience in numerical techniques and /or date analysis would be additional advantage.
Associateship : 22,000/- p.m., plus admissible H.R.A. and Medical benefit.
Age: Below 3 Age : Below 35 years (Relaxable in case of SC/ST/OBC/Women candidates only as per rule).
SELECTION PROCEDURE FOR BOSE INSTITUTE- RESEARCH ASSOCIATE POST:

Candidates can apply on or before 13/4/2015.
No detailed information about the selection procedure is mentioned in the recruitment notification.
HOW TO APPLY FOR RESEARCH ASSOCIATE VACANCY IN BOSE INSTITUTE:

Interested and eligible candidates may read the application procedures and instructions carefully before applying through online as well as submitting the hard copy of the same. Candidates those who has submitted their Ph.D. Thesis and can produce Provisional Ph.D. Certificate at the time of Interview may also apply

Ref
Bose Institute Recruitment 2015 – ADVT. NO. : BI/IF/35/2014-15.

FMLRC: a long-read error correction tool using the multi-string Burrows Wheeler Transform

Neel — Fri, 10 Aug 2018 13:29:28 -0500

FMLRC, or FM-index Long Read Corrector, is a tool for performing hybrid correction of long read sequencing using the BWT and FM-index of short-read sequencing data. Given a BWT of the short-read sequencing data, FMLRC will build an FM-index and use that as an implicit de Bruijn graph. Each long read is then corrected independently by identifying low frequency k-mers in the long read and replacing them with the closest matching high frequency k-mers in the implicit de Bruijn graph. In contrast to other de Bruijn graph based implementations, FMLRC is not restricted to a particular k-mer size and instead uses a two pass method with both a short "k-mer" and a longer "K-mer". This allows FMLRC to correct through low complexity regions that are computational difficult for short k-mers.

Address of the bookmark: https://github.com/holtjma/fmlrc

Which Bioinformatics Journals Do You Follow?

Tenzin Paul — Fri, 10 Apr 2015 12:10:21 -0500

Which are your favorite bioinformatics journals? The ones that you check every month or so, or that you are subscribed to?