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/

RAVEN: a software suite for Matlab that allows for semi-automated reconstruction of genome-scale models

Jit — Wed, 24 Oct 2018 22:38:05 -0500

The RAVEN (Reconstruction, Analysis and Visualization of Metabolic Networks) Toolbox 2 is a software suite for Matlab that allows for semi-automated reconstruction of genome-scale models (GEMs). It makes use of published models and/or KEGG, MetaCyc databases, coupled with extensive gap-filling and quality control features. The software suite also contains methods for visualizing simulation results and omics data, as well as a range of methods for performing simulations and analyzing the results. The software is a useful tool for system-wide data analysis in a metabolic context and for streamlined reconstruction of metabolic networks based on protein homology.

Address of the bookmark: https://github.com/SysBioChalmers/RAVEN

JRF Bioinformatics at DPU, India

Fri, 05 Aug 2016 03:06:26 -0500

Advertisement for position of “JRF (Junior Research Fellow)” on DST research project “Molecular modeling and docking studies on Deguelin and its derivatives with cell cycle arrest, apoptosis and anti-angiogenesis pathway proteins in cancer cell signaling pathway”

Applications are invited on plain paper from eligible candidates along with biodata and copies of certificates in support of age, qualification and experience for the following position:

Particulars Description

1. Position & No. JRF (Junior Research Fellow) 01

2. Title of the Project Molecular modeling and docking studies on Deguelin and its derivatives with cell cycle arrest, apoptosis and anti-angiogenesis pathway proteins in cancer cell signaling pathway

3. Tenure 3 years

4. Investigator Dr. K. V.Swamy

5. Institute Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Tathawade, Pune 411033.

5. Qualifications/Eligibility

Essential: NET (National Eligibility Test) qualified M. Sc Bioinformatics/ M. Tech Bioinformatics/M. Sc Biotechnology/M. Tech Biotechnology or Graduate degree in Professional course with NET qualification or Post graduation degree in professional course

The following examinations conducted by various Central Government Departments/Agencies are considered as National Eligibility Test (NET).

1. CSIR-UGC-LS
2. GATE (Graduate Aptitude Test in Engineering)
3. JAM (Joint Admission Test)
4. GPAT (Graduate Pharmacy Aptitude Test)
5. BET(Biotechnology Eligibility Test)
6. BINC(Bioinformatics National Consortium)
7. JEST( Joint Entrance Screening Test)
8. JGEEBILS(Joint Graduate Entrance Examination for Biology & Interdisciplinary Life Sciences)
9. NBHM Ph.D scholarship Screening Test
10. ICMR- JRF Entrance Examination
11. AICE (ICAR-All India competitive Examination )
(For all above examinations valid score considered at the time of interview)

Desirable: Knowledge and skills in Bioinformatics tools/ softwares

6. Monthly Emoluments Rs.25,000/ (As per DST-SERB rules)

7. Last date for submission of prescribed application 20/08/2016

Kindly send your applications to “Dr. K. V. Swamy, Asst.Professor, Dr. D. Y. Patil Biotechnology & Bioinformatics Institute, Survey No. 87/88, Mumbai-Pune Express Way, Tathawade, Pune - 411033, Maharashtra, India”. Highlight the envelope with “Application for post of JRF (Junior Research Fellow)”.

Note: No TA/DA will be paid for attending the interview.

Advertisement: http://careers.dpu.edu.in/Biotech.aspx

ShinyGO v0.61: Gene Ontology Enrichment Analysis + more

Jit — Wed, 03 Jun 2020 08:00:30 -0500

2/3/2020: Now published by Bioinformatics.

11/3/2019: V 0.61, Improve graphical visualization (thanks to reviewers). Interactive networks and much more.

5/20/2019: V.0.60, Annotation database updated to Ensembl 96. New bacterial and fungal genomes based on STRING-db! Just paste your gene list to get enriched GO terms and othe pathways for over 315 plant and animal species, based on annotation from Ensembl (Release 96), Ensembl plants (R. 43) and Ensembl Metazoa (R. 43). An additional 2031 genomes (including bacteria and fungi) are annotated based on STRING-db (v.10). In addition, it also produces KEGG pathway diagrams with your genes highlighted, hierarchical clustering trees and networks summarizing overlapping terms/pathways, protein-protein interaction networks, gene characterristics plots, and enriched promoter motifs.

Address of the bookmark: http://bioinformatics.sdstate.edu/go/

Research Associate Bioinformatics recruitment in ICGEB, New Delhi

Tue, 16 Aug 2016 03:38:05 -0500

Research Associate Bioinformatics recruitment in ICGEB, New Delhi

Project :“Genetic Transformation and Development of Elite Transgenic Maize (Zea mays L.) for Biotic and Abiotic Stresses Tolerance”.

Qualification: Ph.D. degree in:Biotechnology/Bioinformatics/Biochemistry/Plant Molecular Biology/Plant Physiology/Botany or any related area with evidence of prior experience in maize transformation.

Additional experience in plant transformation of any cereal crop would be preferable.

The appointment would initially be for one year.

How to apply
Interested applicants should send their detailed CV including brief synopsis regarding the previous research experience (along withcontact email address by email) to: Dr. Tanushri Kaul (tanushri@icgeb.res.in). Group Leader, Nutritional Improvement of Crops Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110 067.

Closing date for applications: 22 August 2016.

More at http://www.icgeb.org/vacancies.html