BOL: Related items

Kraken: ultrafast metagenomic sequence classification using exact alignments

Jit — Mon, 27 Jun 2016 11:01:44 -0500

Kraken is an ultrafast and highly accurate program for assigning taxonomic labels to metagenomic DNA sequences. Previous programs designed for this task have been relatively slow and computationally expensive, forcing researchers to use faster abundance estimation programs, which only classify small subsets of metagenomic data. Using exact alignment of k-mers, Kraken achieves classification accuracy comparable to the fastest BLAST program. In its fastest mode, Kraken classifies 100 base pair reads at a rate of over 4.1 million reads per minute, 909 times faster than Megablast and 11 times faster than the abundance estimation program MetaPhlAn. Kraken is available at http://ccb.jhu.edu/software/kraken/.

Krona

https://sourceforge.net/p/krona/home/krona/

Address of the bookmark: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053813/

NIPGR Hires Research Associate, JRF, Laboratory Assistant

Mon, 04 Jul 2016 20:12:14 -0500

National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg - Delhi, Delhi
₹15,000 a month
National Institute of Plant Genome Research (NIPGR) invites applications to recruit on vacant posts of Research Associate (RA), Junior Research Fellow (JRF) and Laboratory Assistant. Applications against these Sarkari Naukri can be submitted on or before 16 July 2016.
NIPGR Vacancy 2016 Details
1. Research Associate (RA)
Qualification: Ph.D. degree (awarded) in Molecular Biology/Biotechnolgy/Biochemistry/Plant Science/ Life Sciences/Bioinformatics or related field with 03 years post-doctoral research experience or 02 research papers in the journals of International repute are eligible to apply. Experience in the area of functional genomics, proteomics, metabolomics, multiomics and system biology will be preferred.
Age Limit: As Per Rules
2. Junior Research Fellow (JRF)
Qualification: M.Sc. degree or equivalent in Biotechnolgy/Biochemistry/Plant Science or Botany/ Life Sciences/Bioinformatics/ Molecular Biology or any other related field. Experience in advanced multiomics, big data analysis, molecular and system biology techniques will be given preference.
Age Limit: As Per Rules
3. Laboratory Assistant
Qualification: B.Sc. degree with 05 years working experience in government R&D Laboratory assisting in the field of molecular biology and genomis.
Pay Scale: Rs.15000/- Per Month
Age Limit: As Per Rules
How to Apply : Duly filled-in applications in prescribed application format along with copies of required documents should be reach to: Dr. Subhra Chakraborty, Staff Scientist-VII, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, P.O. Box NO. 10531, New Delhi – 110067 . The Last Date to submit application is 16 July 2016

Source: http://www.nipgr.res.in/careers/vacancies_latest.php#
Form at http://www.nipgr.res.in/files/careers/format_RA_JRF_LA.doc

Synteny Portal: a web-based application portal for synteny block analysis

Jit — Wed, 24 May 2017 10:39:23 -0500

Synteny Portal, a versatile web-based application portal for constructing, visualizing and browsing synteny blocks. With Synteny Portal, users can easily (i) construct synteny blocks among multiple species by using prebuilt alignments in the UCSC genome browser database, (ii) visualize and download syntenic relationships as high-quality images, (iii) browse synteny blocks with genetic information and (iv) download the details of synteny blocks to be used as input for downstream synteny-based analyses, all in an intuitive and easy-to-use web-based interface. We believe that Synteny Portal will serve as a highly valuable tool that will enable biologists to easily perform comparative genomics studies by compensating limitations of existing tools. Synteny Portal is freely available at http://bioinfo.konkuk.ac.kr/synteny_portal.

http://bioinfo.konkuk.ac.kr/synteny_portal/

Address of the bookmark: http://bioinfo.konkuk.ac.kr/synteny_portal/

RA Bioinformatics at National Bureau of Fish Genetic Resources

Mon, 25 Jul 2016 03:14:06 -0500

F.No. 1(16)/2016-Admn. (DBT-BBSRC Project)
Research Associate /JRF Biotechnology Job vacancies in National Bureau of Fish Genetic Resources on contract basis

Research Associate /01 Post

Essential: Ph.D. in Bioinformatics or 03 years research experience after Post Graduation in Bioinformatics with at least one research paper in Science Citation Indexed (SCI) journals.

Desirable: The candidate should have at least 1st Division during Graduation and Post Graduation. Experience in assembly/ analysis/ annotation of genomic/transcriptomic data generated on next generation sequencing platforms and working knowledge on different genomic softwares. Publications in Relevant Field.

Pay Scale : Rs. 36,000/- +20% HRA

Age: 40 years for male and 45 years for female candidates, as on the date of interview

Junior Research Fellow/ 01

Essential: Master Degree in Biotechnology/Life Science with Specialization in Molecular Biology with NET qualification.

Desirable: Research Experience in Molecular Biology. 1st Division during Graduation as well as Post Graduation. Publications in Relevant Field.

Pay Scale: Rs. 25,000/-+ 20% HRA for 1st and 2nd year and Rs. 28,000/-+ 20% HRA for 3rd year

Age: 35 years for male and 40 years for female candidates, as on the date of interview.
How to apply
A walk-in-interview will be held on 26.07.2016 at 10:00 hrs. at ICAR-National Bureau of Fish Genetic Resources, Lucknow.

More at http://www.nbfgr.res.in/Recruitments.aspx

SOAP2 : Short Oligonucleotide Analysis Package 2

Poonam Mahapatra — Wed, 23 May 2018 10:09:22 -0500

SOAPaligner/soap2 is a member of the SOAP (Short Oligonucleotide Analysis Package). It is an updated version of SOAP software for short oligonucleotide alignment. The new program features in super fast and accurate alignment for huge amounts of short reads generated by Illumina/Solexa Genome Analyzer. Compared to soap v1, it is one order of magnitude faster. It require only 2 minutes aligning one million single-end reads onto the human reference genome. Another remarkable improvement of SOAPaligner is that it now supports a wide range of the read length. SOAPaligner benefitted in time and space efficiency by a revolution in the basic data structures and algorithms used.The core algorithms and the indexing data structures (2way-BWT) are developed by the algorithms research group of the Department of Computer Science, the University of Hong Kong (T.W. Lam, Alan Tam, Simon Wong, Edward Wu and S.M. Yiu).

Address of the bookmark: http://soap.genomics.org.cn/soapaligner.html

EMBOSS Apps

Jit — Wed, 27 Jul 2016 06:00:41 -0500

The programs are listed in alphabetical order, Look at the individual applications or go to the GROUPS page to search by category.

EMBASSY applications are described in separate documentation for each package.

Applications in the current release

Address of the bookmark: http://emboss.sourceforge.net/apps/release/6.6/emboss/apps/

S-plot2: Rapid Visual and Statistical Analysis of Genomic Sequences

Abhimanyu Singh — Tue, 02 Oct 2018 17:57:27 -0500

S-plot2 creates an interactive, two-dimensional heatmap capturing the similarities and dissimilarities in nucleotide usage between genomic sequences (partial or complete). In S-plot2, whole eukaryotic chromosomes and smaller prokaryotic genomes can be efficiently compared. The tool includes functionality to extract, analyze, and automate BLAST queries of regions of interest within the heatmap. This facilitates the investigation of quickly evolving coding regions, novel coding regions, and laterally transferred elements.

Address of the bookmark: https://bitbucket.org/lkalesinskas/splot

SRF and JRF Bioinformatics at Tezpur University, Napaam

Wed, 03 Aug 2016 03:47:38 -0500

Applications are invited for the following temporary positions unde MHRD sponsored Centre of Excellence
in the Department of Computer Science and Engineering (CSE), Tezpur University

Qualification
and Experience : Senior Research Fellow (SRF) and JRF : First Class in M.E/M.Tech in CSE/IT/ECE with research
experience in relevant fields of research (Candidates having valid GATE/NET Score would be preferred).

Fellowship: Rs. 18,000/- per month (fixed)

Duration : 2 (Two) years and may be extended
depending on status of the project

Age Limit: Candidates should not be more than 32 years of
age in case of SRF and 28 years of age in case of JRF and TA. Upper age limit may be relaxed up to 5
years in the case of candidate belonging to SC/ ST/ OBC/ Women/ Differently abled.

How to Apply:
Interested candidates may send their application on plain paper by post along with his/her educational
qualifications, research experience certificates (for SRF), 02 copies of recent passport/stamp size photographs
and contact phone number to Professor D.K Bhattacharyya, Principal Investigator, Department of Computer
Science & Engineering, Tezpur University, Napaam – 784 028, or mail it to dkb@tezu.ernet.in
(or to smh@tezu.ernet.in) within 15 days of publication of this advertisement.

No TA/DA shall
be paid for attending the interview.

For more details: http://www.tezu.ernet.in/ProjectWalkin/Advt-DoRD-CSE-DKB-20-225-6779-A.pdf

WALK-IN INTERVIEW @ JIPMER

Mon, 05 Sep 2016 04:01:13 -0500

Department of Preventive and Social Medicine
, JIPMER, Puducherry –605006

WALK-IN INTERVIEW

JIP/PSM/INDO-US TB/ 2016/

Walk-in-interview for the following vacant posts funded by Department of Biotechnology, Govt.of India for the project entitled “Biomarkers for Risk of Tuberculosis and for Tuberculosis Treatment Failure and Relapse” in the Department of Preventive & Social Medicine, JIPMER, Puducherry.

3. Technical Assistant

MCA/ MSc in Biostatistics/ MSc in Computational Biology from any recognized University @ Rs.23,220 1

Interested candidates may attend the walk-in interview with written screening test on 07, September 2016 at 9.30 A.M in the Dept. of Preventive and Social Medicine, IV Floor, Administrative Block, JIPMER.

The applicants are requested to bring the filled in application form and bio-data with original certificates for verification.

More Info: http://jipmer.edu.in/wp-content/uploads/2016/09/RECRUITEMENTsite-protocol-7.9.2016.pdf

Pango Lineage Analysis !

Abhi — Mon, 15 Nov 2021 03:38:29 -0600

The Pango nomenclature is being used by researchers and public health agencies worldwide to track the transmission and spread of SARS-CoV-2, including variants of concern. This website documents all current Pango lineages and their spread, as well as various software tools which can be used by researchers to perform analyses on SARS-COV-2 sequence data.

Address of the bookmark: https://cov-lineages.org/resources/pangolin/output.html