BOL: Related items

Kalign: fast multiple sequence alignment program for biological sequences.

BioStar — Fri, 01 Nov 2019 00:20:41 -0500

Kalign is a fast multiple sequence alignment program for biological sequences.

Align sequences and output the alignment in MSF format:

kalign -i BB11001.tfa -f msf  -o out.msf

Align sequences and output the alignment in clustal format:

kalign -i BB11001.tfa -f clu -o out.clu

Re-align sequences in an existing alignment:

kalign -i BB11001.msf  -o out.afa

Reformat existing alignment:

kalign -i BB11001.msf -r afa -o out.afa

Address of the bookmark: https://github.com/TimoLassmann/kalign

parallelLastz: Lastz with multi-threads support.

BioStar — Sat, 22 Aug 2020 05:58:40 -0500

Running Lastz (https://github.com/lastz/lastz) in parallel mode. This program is for single computer with multiple core processors.

When the query file format is fasta, you can specify many threads to process it. It can reduce run time linearly, and use almost equal memory as the original lastz program. This is useful when you lastz a big query file to a huge reference like human whole genome sequence.

The program is an extension on the original lastz program which was written by Bob Harris (the LASTZ guy).

Address of the bookmark: https://github.com/jnarayan81/parallelLastz

Research Scientist at IIT Madras

Mon, 07 Mar 2016 04:06:13 -0600

Research Scientist/Project Associate/Project Assistant Jobs opportunity in Indian Institute of Technology Madras (IIT Madras)

Research Scientist

Qualification : Ph.D in any branch of life science or bioinformatics or computational biology Experience : Previous experience in Molecular Biology, Cell Biology, Biochemistry and Genome/big data analysis is desirable but not mandatory

No. of Vacancy : 02

Project Associate

Qualification : MSc in any branch of life science Experience Previous experience in Molecular Biology, Cell Biology and Biochemistry is desirable but not mandatory

No. of Vacancy : 02

Project Assistant

Qualification : BSc in any branch of life science or chemical science Experience Previous experience any branch in Life science, Molecular Biology, Cell Biology and Biochemistry is desirable but not mandatory

No. of Vacancy : 03
How to apply

Interested candidates can forward their profiles to email id: nctb@iitm.ac.in latest by 18th March, 2016

More at https://www.iitm.ac.in/content/national-cancer-tissue-bio-bank-department-biotechnology-iitm-chennai-vacancy-various-post
https://www.iitm.ac.in/sites/default/files/notices/vacancy.pdf

AlfaPang: alignment free algorithm for pangenome graph construction

BioStar — Thu, 28 Aug 2025 02:56:35 -0500

AlfaPang constructs variation graphs, leveraging its alignment-free and reference-free approach, based solely on intrinsic sequence properties. This design allows AlfaPang's runtime and memory usage to scale linearly with the size of input sequences, enabling it to handle significantly larger genome sets compared to other methods.

Address of the bookmark: https://github.com/AdamCicherski/AlfaPang

Research Fellow Bioinformatics at Central University of Rajasthan

Tue, 02 Feb 2016 00:04:50 -0600

Research Fellow Bioinformatics

Eligibility : MSc(Bio-Chemistry, Bio-Informatics, Bio-Tech)
Location : Ajmer
Last Date : 13 Feb 2016
Hiring Process : Face to Face Interview
Central University of Rajasthan

Research Fellow Job vacancies in Central University of Rajasthan

Project Title : “Development of natural product derived febrifugine ananlogues as a novel therapeutics against visceral leishmaniasis”

No. of Post : 01

Qualification : Master of Biochemistry, Biotechnology, Bioinformatics and related biological sciences with minimum 55%, Age limit as per government rule.

Desirable Experience : Candidates with experience in cell culture, Chemoinformatics, and Parasitology will be preferred.

Fellowship : Rs. 25,000/- p.m. consolidated for NET qualified (14,000/- p.m. consolidated for Non-NET)
How to apply

The candidates may apply on a plain paper, along with their curriculum vitae (including name, date of birth, academic qualification starting from 10th class, summary of research experience, email id, phone number and passport size photograph) and email to vkprajapati@curaj.ac.in or post the hard copy to the Dr. Vijay Kumar Prajapati PI, DST-SERB Project (YSS/2015/000716), Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Dist- Ajmer, Rajasthan, 305 817 on or before 13th February 2016.

More at http://www.curaj.ac.in/Default.aspx?PageId=241

Spines

Jitendra Narayan — Tue, 09 Feb 2016 05:07:15 -0600

Spines

Spines is a collection of software tools, developed and used by the Vertebrate Genome Biology Group at the Broad Institute. It provides basic data structures for efficient data manipulation (mostly genomic sequences, alignments, variation etc.), as well as specialized tool sets for various analyses. It also features three sequence alignment packages: Satsuma, a highly parallelized program for high-sensitivity, genome-wide synteny; Papaya, an all-purpose alignment tool for less diverged sequences; and SLAP, a context-sensitive local aligner for diverged sequences with large gaps.

Access Spines here.

http://www.broadinstitute.org/science/programs/genome-biology/spines

Address of the bookmark: http://www.broadinstitute.org/science/programs/genome-biology/spines

Project Assistant/ JRF at North Eastern Hill University

Fri, 12 Feb 2016 09:23:01 -0600

Project Assistant/ JRF

Eligibility : ME/M.Tech, Any Graduate, MSc

Location : Shillong

Last Date : 23 Feb 2016

Hiring Process : Face to Face Interview
North Eastern Hill University

Project Assistant/ JRF Jobs recruitment in North Eastern Hill University on temporary basis

Project Title : "Next Generation Sequencing (NGS)-based de novo assembly of expressed transcripts and genome information of Orchids in North-East India"

Project Assistant

No. of Post : 01

Qualifications : Graduation

Desirable : Experience of working in a Life Science/Plant Biotechnology lab. and familiarity with computers and field work viz. collection of samples.

JRF

No. of Post : 01

Qualifications : M.Tech/M.Sc in Life Sciences/Botany/Biotechnology/ Bioinformatics;

Desirable : Aptitude for Bioinformatics and Computer Programming/ Next generation sequencing data analysis
How to apply

The applications through email bicnehu@gmail.com or post must reach the Dr. Devendra Kumar Biswal, Co-Principal Investigator (Co-PI) within 15 days from the date of publication of this advertisement.

More at http://www.nehu.ac.in/Advertisements/projectVacancy.php

Scientist at Regional Medical Research Centre (ICMR), RMRC, Port Blair

Mon, 22 Feb 2016 04:38:48 -0600

Scientist

Eligibility : MSc, M Phil / Phd, BE/B.Tech

Location : Delhi

Last Date : 08 Mar 2016

Hiring Process : Walk - In
Regional Medical Research Centre -

Notification Order No.1-51/Proj/RMRC/PB/

Scientist – II (Post Code: BIC-II) job position in Regional Medical Research Centre (ICMR)

Essential Qualification: 1 st class Master’s degree in Bioinformatics / Computational Biology. B.E / B.Tech (Bioinformatics / Computer Science / Biotechnology) OR 2nd Class M.Sc. with Ph.D. in Bioinformatics / Computational Biology / Life Science.

Desirable Qualification: Post-doctoral research experience in Bioinformatics / Computational Biology / Computer Science / Life Science at a recognized institution. Experience in handling and analyzing sequencing data. Experience in scripting languages (PERL/PYTHON) etc./ Statistical software. Experience in developing research projects.

Number of Post: 1 UR

Place of Posting: RMRC, Port Blair

Age Limit: 40 years

Pay Scale : Rs.45,954
How to apply

Interested candidates are invited to submit applications along with copies of all the certificates of educational qualifications, date of birth, working experience etc . on the affixing a passport size photograph by Application Format to attend a walk-in interview on 8th March 2016 at 10:30 AM.

More at http://www.icmr.nic.in/icmrnews/port%20blair%20Bioinf%2003-2016.pdf

svelter

Jitendra Prajapati — Mon, 29 Feb 2016 17:33:15 -0600

This software is designed to identify both simple and complex rearrangements from paired-end sequencing data. Users could ran it easily by just alling SVelter.py with proper parameters. It's also possible to ran it on multiple cores by calling different sub-functions separately.

More at https://github.com/mills-lab/svelter/

Address of the bookmark: https://github.com/mills-lab/svelter/

JRF at ICGEB

Fri, 04 Mar 2016 05:34:42 -0600

Vacancy Notice PU/TS/01-16

JRF jobs in International Centre for Genetic Engineering and Biotechnology

Area of research: Computational analysis of protein-protein interactions and metabolic reconstruction of pathways

Qualification : Suitable candidate must have completed Masters in Computer Science/Physics/Mathematics/Bioinformatics or PG diploma in Bioinformatics with very sound programming skills shown in the form of completed project or paper. Programming Skill required: Java/perl/python or any other scripting language and working knowledge of MySQL. Candidate should have some familiarity with R statistical package.

The salary will be as per the guidelines of DBT/DST, based on qualification and experience.

How to apply

Interested candidates may send application along with CV via email to hemant@icgeb.res.in (Dr. Hemant Ritturaj Kushwaha) on or before 08/03/2016. Candidates applying through Email must mention “Application for JRF” in their subject line.

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