BOL: Related items

Project Scientist at National Agri-Food Biotechnology Institute (NABI)

Thu, 25 Aug 2016 05:49:36 -0500

Advt. No. NABI/8(18)/2012-PME-3
Project Scientist recruitment in National Agri-Food Biotechnology Institute (NABI)
Project Title : “Transfer and Evaluation of Indian Banana with Pro-Vitamin A (PVA) Constructs”
Essential qualifications: Ph.D. thesis submitted/awarded in any branch of life/plant sciences. Desirable qualification: a) Excellent academic record with research experience in area relevant to plant metabolic engineering, molecular biology and bioinformatics supported with high quality publications. b) Knowledge and experience of Chromatography and Mass Spectrometry based technological analysis of samples. c) Knowledge and experience of in-silico analysis such as trascriptomics, proteomics and genomics. c) Relevant research publications in reputed international journals with high impact factors.
No. of Post : 01
Age: 35 years
Emoluments: Rs.40,000/- per month.
How to apply
Walk-In-Interview on 29/08/2016 at National Agri-Food Biotechnology Institute, C-127, Industrial Area, Phase VIII, S.A.S. Nagar, Mohali-160 071 Email: siddharth@nabi.res.in

More at http://www.nabi.res.in/Vacancies/NABI/ResearchFellowships/JRFSRFRA/2016/NABI8(18)2012-PME-3/Advt.pdf

ALPACA: A hybrid strategy for assembly of genomic DNA shotgun sequencing reads.

Seema Singh — Mon, 30 Apr 2018 04:38:40 -0500

ALPACA requires Celera Assembler 8.3 or later. It is recommended to build Celera Assembler from source. (Why? The pre-built binaries CA_8.3rc1 and CA8.3rc2 will work for any large data set.

Detail paper at https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3927-8

Address of the bookmark: https://github.com/VicugnaPacos/ALPACA

Useful Bioinformatics Tools

Poonam Mahapatra — Mon, 29 Aug 2016 04:08:12 -0500

Collections of few handy tools for bioinformatician

http://molbiol-tools.ca/Convert.htm

Address of the bookmark: http://molbiol-tools.ca/Convert.htm

PERGA: A Paired-End Read Guided De Novo Assembler for Extending Contigs Using SVM and Look Ahead Approach

Rahul Nayak — Tue, 05 Jun 2018 09:57:11 -0500

PERGA - Paired End Reads Guided Assembler PERGA is a novel sequence reads guided de novo assembly approach which adopts greedy-like prediction strategy for assembling reads to contigs and scaffolds. Instead of using single-end reads to construct contig, PERGA uses paired-end reads and different read overlap sizes from O ≥ Omax to Omin to resolve the gaps and branches. Moreover, by constructing a decision model using machine learning approach based on branch features, PERGA can determine the correct extension in 99.7% of cases. PERGA will try to extend the contigs by all feasible nucleotides and determine if these multiple extensions due to sequencing errors or repeats by using looking ahead technology, and it also try to separate the different repeats of nearby genomic regions to make the assembly result more longer and accurate. The simulated E.coli paired-end reads data are generated using GemSim (KE McElroy, F Luciani, T Thomas. Gemsim: General, Error-Model Based Simulator of Next-Generation Sequencing Data. BMC Genomics 2012, 13:74), with coverage 50x, 60x, 100x, read lengths 100-bp, and can be downloaded from https://github.com/zhuxiao/data_PERGA.

Address of the bookmark: https://github.com/hitbio/PERGA

Artemis Comparison Tool (ACT)

Shruti Paniwala — Wed, 07 Sep 2016 03:54:41 -0500

ACT is a Java application for displaying pairwise comparisons between two or more DNA sequences. It can be used to identify and analyse regions of similarity and difference between genomes and to explore conservation of synteny, in the context of the entire sequences and their annotation. It can read complete EMBL, GENBANK and GFF entries or sequences in FASTA or raw format.

Address of the bookmark: http://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act

ASplice: a scalable and memory-efficient algorithm for de novo transcriptome assembly

Rahul Nayak — Tue, 03 Jul 2018 04:09:46 -0500

With increased availability of de novo assembly algorithms, it is feasible to study entire transcriptomes of non-model organisms. While algorithms are available that are specifically designed for performing transcriptome assembly from high-throughput sequencing data, they are very memory-intensive, limiting their applications to small data sets with few libraries. Texas A&M University researchers develop a transcriptome assembly algorithm that recovers alternatively spliced isoforms and expression levels while utilizing as many RNA-Seq libraries as possible that contain hundreds of gigabases of data. New techniques are developed so that computations can be performed on a computing cluster with moderate amount of physical memory. Availability – A software program that implements the algorithm is available at: http://faculty.cse.tamu.edu/shsze/asplice. Sze SH, Pimsler ML, Tomberlin JK, Jones CD, Tarone AM. (2017) A scalable and memory-efficient algorithm for de novo transcriptome assembly of non-model organisms. BMC Genomics 18(Suppl 4):387.

Address of the bookmark: http://faculty.cse.tamu.edu/shsze/asplice/

Traineeship/Studentship conducts University of Delhi (Gargi College)

Mon, 05 Sep 2016 03:45:58 -0500

Traineeship/Studentship cunducts University of Delhi (Gargi College) on purely temporary for a period of six months.
Traineeship — 01 (one post)
Essential Qualification: Post Graduate degree in Bioinformatics or any other branch of Life Sciences preferably with dissertation in Bioinformatics. Desirable Qualification: Prior knowledge of programming languages such as C, VB, SQL etc. and software/database development
Studentship- 01 (one post)
Essential Qualifications: Final year Post Graduate students pursuing a degree in Bioinformatics or any branch of Life Science with knowledge of bioinformatics
Salary: Rs.8000/- p.m.
How to apply
Interested candidates are required to appear for the walk in interview on 14th. September, 2016 at 9.30 AM in Principal's Office, Gargi College, Sirifort Road, N. Delhi-110049

More at http://www.du.ac.in/du/index.php?mact=News,cntnt01,detail,0&cntnt01articleid=12859&cntnt01returnid=83

Nanopolis: polish a genome assembly

Rahul Nayak — Thu, 26 Jul 2018 04:51:28 -0500

Software package for signal-level analysis of Oxford Nanopore sequencing data. Nanopolish can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs and indels with respect to a reference genome and more (see Nanopolish modules, below).

Quickstart

http://nanopolish.readthedocs.io/en/latest/quickstart_consensus.html

Algorithms

http://simpsonlab.github.io/2017/06/30/nanopolish-v0.7.0/

Address of the bookmark: https://github.com/jts/nanopolish

Sybil

Jit — Wed, 07 Sep 2016 03:20:44 -0500

The Sybil software package provides a primarily web-based front-end to comparative genome datasets warehoused in a chado relational database. It was developed by the bioinformatics department at The Institute for Genomic Research (TIGR) and development continues at the J. Craig Venter Institute (JCVI) and the Institute for Genome Sciences (IGS) at the University of Maryland: Baltimore. Sybil has been used at TIGR/JCVI, IGS, NYU, New York Medical College, Novartis Vaccines and University of Maryland: College Park to support a number of research projects that involve comparative genome analysis. The following sections provide some high-level technical details about the overall architecture and external dependencies of the Sybil package.

Address of the bookmark: http://sybil.sourceforge.net/

Bioinformatics openings at Sri Venkateswara College, University of Delhi

Tue, 20 Sep 2016 05:43:24 -0500

Bioinformatics center

Sri Venkateswara College (University of Delhi)

New Delhi- 110021

1. Junior Research Fellow (1 Post)

Applications are invited for the post of Junior Research Fellow (JRF) under DST funded project which is purely temporary and is strictly for project duration only.

Title of project

No. of post

Remuneration (Rs.)

“Computational assisted Design and Synthesis of Novel Antimalarial Agents Embodying Structural Diversity Suitable for Protease Inhibitors”

(One)

Fellowship and HRA as per DST guidelines

Qualification

Post Graduate Degree in Basic Science (M.Sc./M.Tech in Bioinformatics/Biophysics) from a recognized University in India or abroad with at least 55% marks with NET qualification or Graduate Degree in Professional Course with NET Qualification or Post Graduate Degree in Professional Course.

Desirable

Fair knowledge of Computer Aided Drug Designing (CADD), Protein Structure modeling, molecular docking, and simulations are preferable.

2. Traineeship (1 Post)

Applications are invited for the position of traineeship in DBT-BTISnet funded Bioinformatics Infrastructure Facility (BIF) to carry out project work in the area of Bioinformatics.

Qualification

Applicant should be possess PG degree/PG diploma in Bioinformatics for traineeship. The traineeship is awarded for a period of six months from the date of joining and is not extendable. The selected candidates are entitled to receive a stipend of Rs. 8000/- per month (consolidate) for a period of 6 months.

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3. Studentship (1 Post)

Applications are invited for the position of Studentship in DBT-BTISnet funded Bioinformatics Infrastructure Facility (BIF) to carry out project work in the area of Bioinformatics.

Qualification

Candidates pursuing the Final Year of Post Graduate Degree in Basic Science (M.Sc.) or Post Graduate/ Graduate Degree in Professional Course (M.Tech/B.Tech) in Bioinformatics from a recognized University in India or abroad. The selected candidates are entitled to receive a stipend of Rs. 8000/- per month (consolidate) for a period of 6 months.

How to Apply?

Applicants are required to send applications on plain paper, stating the name, address, date of birth, educational qualification, experience and Institute, along with attested photocopies of mark sheets and certificates etc. by September 20, 2016 to:

The Coordinator

Bioinformatics Center, Sri Venkateswara College

Benito Juarez Road, Dhaula Kuan, New Delhi- 110021

Applications may also be sent by email to contact@bic-svc.ac.in. Strictly mention "Application for JRF, Traineeship or Studentship" in the subject line as the case may be.

Short listed candidates will be called for an interview. Canvassing in any form will be a disqualification. No TA/DA will be paid either for attending the interview or joining the post.

For more details visit our lab webpage: http://www.bic-svc.ac.in