BOL: Related items

zPicture: A dynamic blastz alignment visualization

Archana Malhotra — Tue, 30 Jan 2018 16:03:08 -0600

zPicture is a dynamic alignment and visualization tool that is based on blastz alignment program utilized by PipMaker. zPicture alignments can be automatically submitted to rVista 2.0 to identify conserved transcription factor binding sites.

Address of the bookmark: https://zpicture.dcode.org/

Assistant Professor - Computational Biology and Bioinformatics in Navi Mumbai

Fri, 04 Dec 2015 20:40:59 -0600

No. ACTREC / ADVT-A/2/2015
Pay in Pay band and Grade Pay : PB-3 (Rs 15,600-39,100) Pay in pay band Rs 21,900+ G.P. of Rs 7,600
Total emoluments = 82,000/- p.m. & nbsp
Educational Qualification : Ph.D. or MD/Ph.D.
Experience : Post MD / Ph.D. Research experience of 5 years The last date of application submission is January 15th, 2016.
Interested candidates shall send the applications through email: office.sao(at)actrec.gov.in.
For More Details : www.actrec.gov.in/data%20files/Vacancies/2015/Faculty-Positions-SOE-24-11-15.pdf

LAMSA: fast split read alignment with long approximate matches

Jit — Tue, 15 May 2018 04:44:42 -0500

LAMSA (Long Approximate Matches-based Split Aligner) is a novel split alignment approach with faster speed and good ability of handling SV events. It is well-suited to align long reads (over thousands of base-pairs). LAMSA takes takes the advantage of the rareness of SVs to implement a specifically designed two-step strategy. That is, LAMSA initially splits the read into relatively long fragments and co-linearly align them to solve the small variations or sequencing errors, and mitigate the effect of repeats. The alignments of the fragments are then used for implementing a sparse dynamic programming (SDP)-based split alignment approach to handle the large or non-co-linear variants. We benchmarked LAMSA with simulated and real datasets having various read lengths and sequencing error rates, the results demonstrate that it is substantially faster than the state-of-the-art long read aligners; mean-while, it also has good ability to handle various categories of SVs. LAMSA is open source and free for non-commercial use. LAMSA is mainly designed by Bo Liu & Yan Gao and developed by Yan Gao in Center for Bioinformatics, Harbin Institute of Technology, China.

Address of the bookmark: https://github.com/hitbc/LAMSA

ArrayGen Next Generation Genome Browser Coming Soon !!!

ArrayGen Technologies — Thu, 03 Dec 2015 05:52:09 -0600

The ANG genome browser is a visualization tool, developed by ArrayGen Technologies. This is a fast and an efficient genome browser, built with Javafx and Java swing. ANG genome browser was built for latest next generation sequencing data analysis. It is platform independent and much simpler to use.

The main features are, it supports many standard file formats such as GFF, BED, GTF, FASTA, VCF, BAM and it can be integrated with other browsers or tools for analysis of genome.

SRF/JRF Bioinformatics at CIARI

Fri, 04 Dec 2015 00:10:09 -0600

Realizing the importance of Island Agriculture to meet the requirements of local population and tourists, Indian Council of Agricultural research (ICAR) established Central Island Agricultural Research Institute, Port Blair on June 23rd, 1978 by merging different regional research stations of ICAR institutes located in Islands. The ultimate aim of CIARI is the developments of island agricultural production technologies which utilizes the strengths of the island and convert the constraints in opportunities, without causing any ill effect to the fragile ecosystem of the island.The institute has made tremendous progress in the Agriculture development of the islands during the last three decades. Keeping in view the natural resources of the islands diversity, fragile ecosystem, research program would be designed to maximize the productivity without disturbing to the islands ecosystem to provide better and decent livelihood and as a source of revenue and resource generation. Research and development in Agriculture sector should cover all disciplines in order to have a balanced progress in all disciplines for the overall benefits of the farmers of these islands.

Position I

Job Title : Junior Research Fellow

No. of Posts : One

Project : Establishment of sub distributed information centre

Qualification : M.Sc in Basic Science with NET or B.Sc in professional course with NET or M.Sc in professional course

Desired Experience : Experience in Bioinformatics and molecular biology

Payscale : Rs. 25000 per month

Age Limit : Upto 35 for men and 40 for women with 5 years relaxation to SC/ST and 3 years relaxation for OBC.

Position II

Job Title : Traineeship

No. of Posts : One

Project : Establishment of sub distributed information centre

Qualification : B.Sc Bioinformatics /Biotechnology / Life Science / Computer Science

Desired Experience : Experience in Bioinformatics and molecular biology

Payscale : Rs. 8000 per month

Age Limit : Upto 35 for men and 40 for women with 5 years relaxation to SC/ST and 3 years relaxation for OBC.

Position III

Job Title : Studentship

No. of Posts : Two

Project : Establishment of sub distributed information centre

Qualification : B.Sc Bioinformatics /Biotechnology / Life Science / Computer Science

Desired Experience : Experience in Bioinformatics and molecular biology

Payscale : Rs. 8000 per month

Age Limit : Upto 35 for men and 40 for women with 5 years relaxation to SC/ST and 3 years relaxation for OBC.

How to Apply : Candidates who meet the requirements can attend the walk in interview at CIARI,Port Blair on 09.12.2015 10.30AM.

http://icar-ciari.res.in/employment/9-12-15.pdf

Post-doc position at LABGeM - Evry, France

Fri, 11 Dec 2015 06:24:00 -0600

The LABGeM team (CEA/Genoscope, CNRS UMR 8030, France, Dir. Claudine Médigue) is developing integrated approaches which combines bioinformatics methods based (i) on genomic and metabolic contexts, (ii) on an orignal metabolic network representation and (iii) on a structural classification of active sites for the discovery of new metabolic enzymatic activities.

We are hiring a post-doctoral fellow for the development of innovative bioinformatics methods to explore metabolic networks and enzyme families. These methods will be based on protein family analysis and graph approaches combining genomic and metabolic contexts.

For more details, please see this link : http://goo.gl/tHQOqk

Qualifications:
PhD degree in bioinformatics or computational biology
- Previous experience in network or protein family analysis
- Programming skills (C/C++, Python, Java) and in common biostatistical analyses
- Team player, innovative and creative thinking, good oral and written communication skills

24 months, Post Doctoral position
Start: from March 2016
Place: CEA, Genoscope UMR8030, LABGeM (Laboratory of Bioinformatics Analyses for Genomics and Metabolism), Evry, France
Contact: David Vallenet, vallenet@genoscope.cns.fr
Publications: https://scholar.google.com/citations?user=rJNPLSAAAAAJ
Remuneration per month: from 2,850 €

Interested candidates should send their CV, statement of research interests, and contact information of at least 2 references to David Vallenet (vallenet@genoscope.cns.fr).

Cactus: a reference-free whole-genome multiple alignment program

Jit — Mon, 12 Aug 2019 07:52:33 -0500

Cactus is a reference-free whole-genome multiple alignment program. The principal algorithms are described here: https://doi.org/10.1101/gr.123356.111

Cactus uses substantial resources. For primate-sized genomes (3 gigabases each), you should expect Cactus to use approximately 120 CPU-days of compute per genome, with about 120 GB of RAM used at peak. The requirements scale roughly quadratically, so aligning two 1-megabase bacterial genomes takes only 1.5 CPU-hours and 14 GB RAM.

Address of the bookmark: https://github.com/ComparativeGenomicsToolkit/cactus

Microscope

Jitendra Narayan — Fri, 04 Mar 2016 05:26:31 -0600

Microscope Platform user documentation.

The MicroScope platform is available at this URL:

https://www.genoscope.cns.fr/agc/microscope

Address of the bookmark: http://microscope.readthedocs.org/en/latest/index.html

The wavefront alignment (WFA) algorithm

BioStar — Sun, 28 Jun 2020 10:17:50 -0500

The wavefront alignment (WFA) algorithm is an exact gap-affine algorithm that takes advantage of
homologous regions between the sequences to accelerate the alignment process. As opposed to traditional dynamic programming algorithms that run in quadratic time, the WFA runs in time O(ns), proportional to the read length n and the alignment score s, using O(s^2) memory. Moreover, the WFA exhibits simple data dependencies that can be easily vectorized, even by the automatic features of modern compilers, for different architectures, without the need to adapt the code.

Address of the bookmark: https://github.com/smarco/WFA

PostDoc at IISER -TVM

Fri, 26 Feb 2016 03:53:05 -0600

Postdoctoral Fellowship/ Research Associateship

Eligibility : M Phil / Phd

Location : Thiruvananthapuram

Last Date : 30 Apr 2016

Hiring Process : Face to Face Interview
IISER -TVM

The Postdoctoral Fellowship/Research Associateship is a full-time, contractual position for highly qualified young scientists to carry out research at CCMS, IISER-TVM.

Research areas at the Centre

Quantum Chemistry/ Computational Fluid Dynamics/Condensed Matter Physics (Theory)/Genomics/Genetics/Gravitational Waves

Qualifications: PhD in Bioinformatics / Biophysics / Physics / Astrophysics / Chemistry / Mathematics / Engineering (Mechanical/Aerospace) Those who are in the final stages of their Ph.D. thesis submission are also eligible to apply. However, those candidates must have submitted the thesis at the time of the interview.

Experience: Applicants should have at least three peer reviewed publications and relevant experience in the research area they are applying for.

No. of positions: 5

Age limit: 35 yrs or below. A relaxation of 5 yrs will be applicable to candidates belonging to SC/ST/OBC and women candidates

Salary: The Fellowship carries a remuneration of INR Rs. 5,18,000 - Rs. 5,76,000 per annum (including HRA). The postdoctoral fellowship may not be held concurrently with any other national or international fellowships. It is also not transferable to any other fellowship
How to apply

Applications should reach the Head, CCMS, IISER Thiruvananthapuram,CET Campus, Engineering College PO,Thiruvananthapuram 695016 on or before April 30, 2016 by e-mail to ccms@iisertvm.ac.in by mentioning the research area name in the subject line.

More at http://www.iisertvm.ac.in/openings/read_opening/150.phpx