BOL: Related items

Pacasus: Correction of palindromes in long reads from PacBio and Nanopore

BioStar — Mon, 12 Nov 2018 05:26:48 -0600

Tool for detecting and cleaning PacBio / Nanopore long reads after whole genome amplification. Check the poster from the Revolutionizing Next-Generation Sequencing (2nd edition) conference in the source folder: https://github.com/swarris/Pacasus/blob/master/vib2017.pdf.

The prepint version is found on http://www.biorxiv.org/content/early/2017/08/09/173872

It uses the pyPaSWAS framework for sequence alignment (https://github.com/swarris/pyPaSWAS)

Address of the bookmark: https://github.com/swarris/Pacasus

RA Bioinformatics at NIPGR

Tue, 20 Oct 2015 04:11:56 -0500

Applications are invited from suitable candidates for filling up the purely temporary positions of one Research Associate (RA) and one Junior Research Fellow (JRF) in the DBT Part-B Sub-project-1&2 entitled Transcriptome and epigenome diversity analysis during seed development for discovery of molecular markers and gene regulatory mechanism in chickpea of Seed Biology

Research Associate (one post): Emoluments as per DST/DBT norms & as sanctioned in the project
Qualification: Candidates having Ph.D. degree (awarded) in Life Sciences/Molecular Biology/Bioinformatics or related field are eligible to apply.

Junior Research Fellow (one post): Emoluments as per DST/DBT norms & as sanctioned in the project
Qualification: Candidates having M.Sc. degree or equivalent (with minimum 55% marks) in Life Sciences, Biotechnolgy, Bioinformatics, Molecular Biology or any other related field are eligible to apply

Additional Information

Address:
Staff Scientist
National Institute of Plant Genome Research (NIPGR)
Aruna Asaf Ali Marg, P.O. Box NO. 10531,
New Delhi - 110067

States & U.T
State & Union Territories Delhi

How To Apply

Apply Details
Eligible candidates may apply by sending their complete application in the given format. The attested copies of the certificates and proof of research experience (if any) are to be attached with the hard copy of application. The applications should reach at the address given below within 15 days from the date of advertisement.

Web/Notification URL
http://www.nipgr.res.in/careers/vacancie s_latest.php

ngs-bits - Short-read sequencing tools

Neel — Thu, 16 Jan 2020 23:14:00 -0600

Binaries of ngs-bits are available via Bioconda. Alternatively, ngs-bits can be built from sources:

Binaries for Linux/macOS
From sources for Linux/macOS
From sources for Windows

Address of the bookmark: https://github.com/imgag/ngs-bits

Project Assistant BioInformatics

Mon, 02 Nov 2015 03:23:09 -0600

Project Assistant BioInformatics

Eligibility : ME/M.Tech(Bio-Informatics/Bio-Chemistry Engg), MSc(Bio-Informatics), BE/B.Tech

Location : Pune

Last Date : 16 Nov 2015

Hiring Process : Face to Face Interview

No. Bio/NCIM/3

Project Assistant II Jobs opportunity in National Chemical Laboratory (NCL) on temporary basis

Project Code No. : GAP312626

Title of the Project : Microbial ecology and distribution of geochemical cycling genes in an hot spring ecosystem

No. of Post : 01

Qualifications : M.Sc./B.Tech/M.Tech in Computational biology/ Bioinformatics from recognized university with minimum 60 % marks (aggregate)

Desirable : Good knowledge of computational skills, Linux (command line and GUI) and Unix; Perl / Python / R /C-programming. Practical knowledge of analysis of Next generation sequence datasets (amplicon sequencing, whole metagenome, and complete genome sequencing) with reference to microbes. Analysis and statistical validation of NGS data generated from different chemistry platforms. Some wet-lab experience in microbial system would be an added advantage as project involves some travel.

Emoluments : Rs. 16,000/-

Age Limit : 28 years

The application with the above information duly signed together with photo-copies of relevant certificates/testimonials should be addressed to : The Head, NCIM Resource Centre (Attn Dr. M.S. DHARNE), National Chemical Laboratory, Pune 411 008, so as to reach on or before 16th November 2015.

More at http://www.ncl-india.org/files/JoinUs/JobVacancies/TemporaryJobs.aspx?menuid=ql6&childmenustripid=divSubQL6

NCBI PSI-BLAST Tutorial

Fri, 23 Aug 2013 02:25:02 -0500

http:--www.biotechnology.jhu.edu- Tutorial for PSI-BLAST, an extension of BLAST that uses matrix algebra. BLAST is a cornerstone bioinformatics tool at NCBI. BLAST is the Basic Local Alignment Search tool and will protein and DNA sequences that are related to a sequence that the user provides.

Pre- or postdoctoral research fellowship in Structural Bioinformatics at Padova

Thu, 05 Nov 2015 22:15:12 -0600

A research fellowship for a software developer is available at the BioComputing UP Laboratory, University of Padova (URL: http://protein.bio.unipd.it/).
A highly motivated and creative candidate is sought to work on structural bioinformatics. Specifically, the project entails the development of novel methods, tools and databases for the analysis of protein structures.

The BioComputing UP Laboratory, headed by Prof. Silvio Tosatto, is a dynamic group of a dozen people working on several aspects of prediction of protein structure & function employing techniques at the intersection between biology, medicine, chemistry, physics & computer science.
Our aim is to integrate the development of novel methods and their application to biologically relevant problems.

We are looking for candidates with a solid Bioinformatics background, programming experience (Python, C++ and/or Java) and good knowledge of molecular biology (protein structure/function). Good knowledge of statistics as well as experience in using database systems (MongoDB, MySQL and/or Postgres) is desirable. Candidates should have a degree with top marks, optionally hold a PhD, and be highly motivated to work on interdisciplinary research. Good knowledge of English, an open-minded spirit, being collaborative and creative are crucial.

The fellowship, which should start as soon as possible, is renewable and initially for one year. It will be commensurate to experience, can be extended depending on performance and may lead to a PhD degree. The successful candidate will be working full-time at the BioComputing UP Laboratory, University of Padova. Travel support for conferences and/or research visits abroad is provided.
To apply, please send your CV, with a motivation letter and brief description of your research background as well as the names of two (or more) references to: biocomp@bio.unipd.it.

Start date: As soon as possible

Duration: 1 year, renewable

Salary on grant: Commesurate to experience

Contact Person (Referent): Silvio Tosatto

Ref. E-Mail: biocomp@bio.unipd.it

Tel: +39 049 827 6269
Fax: +39 049 827 6260

Group Web Page: http://protein.bio.unipd.it/

Sequence - Evolution - Function; Computational Approaches in Comparative Genomics

Jit — Sun, 06 Aug 2017 06:58:12 -0500

Sequence - Evolution - Function is an introduction to the computational approaches that play a critical role in the emerging new branch of biology known as functional genomics. The book provides the reader with an understanding of the principles and approaches of functional genomics and of the potential and limitations of computational and experimental approaches to genome analysis.

Address of the bookmark: https://www.ncbi.nlm.nih.gov/books/NBK20260/

LAST

Archana Malhotra — Wed, 09 Mar 2016 14:27:01 -0600

LAST can:

Handle big sequence data, e.g:
- Compare two vertebrate genomes
- Align billions of DNA reads to a genome
Indicate the reliability of each aligned column.
Use sequence quality data properly.
Compare DNA to proteins, with frameshifts.
Compare PSSMs to sequences
Calculate the likelihood of chance similarities between random sequences.
Do split and spliced alignment.
Train alignment parameters for unusual kinds of sequence (e.g. nanopore).

Address of the bookmark: http://last.cbrc.jp/

Sequence Tube Maps: displays multiple genomic sequences in the form of a tube map

Jit — Wed, 11 Mar 2020 01:12:06 -0500

A JavaScript module for the visualization of genomic sequence graphs. It automatically generates a "tube map"-like visualization of sequence graphs which have been created with vg. (https://github.com/vgteam/vg)

Link to working demo: https://vgteam.github.io/sequenceTubeMap/

Address of the bookmark: https://github.com/vgteam/sequenceTubeMap

Traineeship at Biomedical Informatics Centre PGIMER Chandigarh

Sun, 29 Nov 2015 03:04:27 -0600

Biomedical Informatics Centre

PGIMER

Chandigarh

invites application for a project dissertation program for students who have completed their first year of M.Sc. in Bioinformatics.

This is an exciting opportunity for Master's students to train in modern methods in Bioinformatics. The duration of the training will be four to six months, starting from January 2016.

Education: Pursuing M.Sc. Bioinformatics

Essential: Post graduate applicants should have completed their first year and should be in the third semester or first half of the second year.

Only students who are willing to spend a minimum period of 4 months to a maximum of six months, without any break, would be eligible for the program.

How to Apply: Candidates interested in the above project dissertation program should apply online. Send your CV, Scanned copy of letter of recommendation from Head of Institution along with Registration form in the given format should be sent to: info@bicpgi.org

Please mention clearly “Project dissertation & your Name” in the Subject.

The last date for application is December 23, 2015

Note: Selected candidates may please note that the program is free of cost and would not provide any financial aid for transport and stay. Name of the selected candidates would be posted on the centre website by December 31, 2015.

Incomplete applications will be rejected.

For more information visit our website: http://bic-pgi.org/