BOL: Related items

ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information

BioJoker — Sun, 20 Jan 2019 06:34:36 -0600

ClipCrop for detecting SVs with single-base resolution using soft-clipping information. A soft-clipped sequence is an unmatched fragment in a partially mapped read. To assess the performance of ClipCrop with other SV-detecting tools, we generated various patterns of simulation data – SV lengths, read lengths, and the depth of coverage of short reads – with insertions, deletions, tandem duplications, inversions and single nucleotide alterations in a human chromosome.

Address of the bookmark: https://github.com/shinout/clipcrop

JRF/SRF at University of Calcutta

Fri, 31 Oct 2014 08:53:10 -0500

Applications are invited to appear at a walk-in-interview for one post of Junior Research Fellow in the DBT(DBT Twinning NER) sponsored project entitled “Protein folding kinetics is a selection force on shaping codon usage bias in the high expression genes” in the room of the HOD, Department of Biotechnology and the Coordinator, DR. B. C. Guha Centre for Genetic Engineering and Biotechnology, University College of Science, 35 Ballygunge Circular Road, Kolkata 700019 on the 12th November, 2014 at 3:00 p.m.

Essential qualifications: First class M. Sc. in any branch of life sciences and qualified CSIR-UGC NET/GATE Examination.

Desirable qualifications: Practical experience in biochemical and biophysical studies of proteins

Emoluments: as per DBT norms

The project is tenable for two years, initially for one year.

Age: Below 28 years (relaxable in the case of SC/ST/OBC/women candidates)

Candidates are requested to bring two sets of complete applications on plain paper furnishing bio-data and copies of attested certificates along with originals (for verification) on the date of interview.

No TA/DA is admissible for candidates appearing at the interview.

Dr. Rajat Banerjee
Assistant Professor
Department of Biotechnology and
Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology
University College of Science
35, Ballygunge Circular Road
Kolkata 700019

Advertisement: www.caluniv.ac.in/news/jrf_biotech_2.pdf

Minipolish: A tool for Racon polishing of miniasm assemblies

BioStar — Tue, 03 Dec 2019 02:40:54 -0600

Miniasm is a great long-read assembly tool: straight-forward, effective and very fast. However, it does not include a polishing step, so its assemblies have a high error rate – they are essentially made of stitched-together pieces of long reads.

Racon is a great polishing tool that can be used to clean up assembly errors. It's also very fast and well suited for long-read data. However, it operates on FASTA files, not the GFA graphs that miniasm makes.

That's where Minipolish comes in. With a single command, it will use Racon to polish up a miniasm assembly, while keeping the assembly in graph form.

It also takes care of some of the other nuances of polishing a miniasm assembly:

Adding read depth information to contigs
Fixing sequence truncation that can occur in Racon
Adding circularising links to circular contigs if not already present (so they display better in Bandage)
'Rotating' circular contigs between polishing rounds to ensure clean circularisation

Address of the bookmark: https://github.com/rrwick/Minipolish

JRF in Bioinformatics @ Pondicherry University

Sat, 08 Nov 2014 14:34:48 -0600

Eager to get JRF job in Puducherry? Pondicherry University, School of Life Sciences, Centre for Bioinformatics has issued notification to fill the vacancy of JRF for DST sponsored research project entitled "Design and discovery of aurora kinase inhibitors as anti cancer drugs; application of computer aided drug design". It is good chance to get job with Pondicherry University and secure your future. Learn eligibility criteria and apply on or before 21.11.2014.

Required Skills: no special skills required for this job post
Required Experience:
Experience in computer aided drug design and or biochemical testing of natural or synthetic compounds is desired
Required Education:
M.Sc. / M.Tech.

Required Job Profile:
Candidate must possess M.Sc. in bioinformatics or computational biology or biotechnology or any branch of life sciences or pharmacology or chemical sciences or M.Tech. in any branch of life sciences with at least fifty five percent marks with NET or GATE.

Desired Job Profile:
Candidate having experience in computer aided drug design and or biochemical testing of natural or synthetic compounds.

How to apply:
Eligible and interested candidates should need to appear for walk-in interview on 21.11.2014 at 1700 hrs at the above mentioned address.

Contact
Pondicherry University
Dr. S. Mohane Coumar, Assistant Professor & Project Investigator, Centre for Bioinformatics, Pondicherry University, Puducherry 605 014
Email:registrar@pondiuni.edu.in
Phone: 0413-2655175

More at http://www.pondiuni.edu.in/sites/default/files/JRF-bioinfor-041114.pdf

HASLR: a tool for rapid genome assembly of long sequencing reads

LEGE — Fri, 31 Jan 2020 05:50:15 -0600

HASLR is a tool for rapid genome assembly of long sequencing reads. HASLR is a hybrid tool which means it requires long reads generated by Third Generation Sequencing technologies (such as PacBio or Oxford Nanopore) together with Next Generation Sequencing reads (such as Illumina) from the same sample.

Address of the bookmark: https://github.com/vpc-ccg/haslr

PhD opportunity / AiCADD fellowship (MHRD, Govt. of India) of University of Kerala.

Sat, 08 Nov 2014 15:16:24 -0600

No. DCB/DBT-BIF/229 /14-15 07-11-2014

Applications are invited for the AiCADD fellowship (MHRD, Govt. of India) of University of Kerala.

The terms and conditions of the fellowship is given below:

Ø The AiCADD PhD Fellowship scheme will be available for the students registered for full-time research or intending to register and pursue full time research at SIUCEB in frontier areas of bioinformatics, computational biology, systems biology and closely allied areas with focus on Ayur-Informatics.

Ø The fellowships will be widely announced and open to students irrespective of geographical consideration.

Ø Candidates availing of this fellowship shall not be in receipt of any other fellowships concurrently.

Ø Researchers will be selected on the basis of research aptitude test and personal interview.

Ø Each selected student will be eligible for a monthly fellowship of Rs. 10,000/- for the 1st and 2nd year and Rs. 12,000/- for the 3rd year.

Ø Candidates must register for PhD within one year of joining, failing which the fellowship will have to be remitted back.

Ø Candidates receiving the fellowship shall submit bi-annual reports of progress and the continuation of the fellowship will be based on the evaluation of the same.

Ø Candidates are also required to take up academic duties including teaching upto a maximum of 6 hours per week, as directed by AiCADD Principal Investigator.

Interested candidates may please forward their application along with resume on or before 15th November 2014 in the following address. Principal Investigator, AiCADD Centre, Dept. of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram - 695581.

More at https://sites.google.com/site/centreforbioinformatics/announcements

GSP4PDB: a web tool to visualize, search and explore protein-ligand structural patterns

Neel — Sun, 15 Mar 2020 03:41:12 -0500

GSP4PDB is a user-friendly and efficient application to search and discover new patterns of protein-ligand interaction.

GSP4PDB is part of the services provided by the Bioinformatic Group of the University of Talca

http://gdblab.com/gsp4pdb/gsp4pdb2/

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3352-x

Address of the bookmark: http://gdblab.com/gsp4pdb/gsp4pdb2/

Sr.Bioinformatics Analyst (NGS) at Ocimum Biosolution

Sat, 15 Nov 2014 04:46:10 -0600

“Ocimum Biosolution” is a comprehensive Integrated Life Science Informatics solutions provider with service offerings that span Sample and Data Management (LIMS, Biologics Data Management), Genomics Data Analysis Services such as Gene Expression, Genotyping, and Next Gen Sequencing, Bioinformatics and Genomics Databases (BioExpress®, ToxExpress®) and Bio-IT consulting services.

Experience Required: 3-5 years of experience

No of Positions : Multiple

Qualifications: Candidates with minimum qualification as M.Sc Bioinformatics with 3-5 years of experience in Life sciences R&D or Pharma Industry.

Ph.D candidates with research experience in Bioinformatics with publications in International journal and minimum 2 years of industry experience in clinical genomics will be preferred for this position.

Requirement:

1. Must have basic understanding of molecular biology and Genomics.

2. Experience in application development or must have expertise in programming using either of Perl/Python.

3. Experience in statistical programming using R/Bioconductor/Matlab.

4. Strong concept in statistical and mathematical modelling.

5. Experience in designing and developing the bioinformatics pipeline.

6. Must have minimum 2+ years of hands on experience in NSG data analysis such as RNA-Seq,Exome-Seq ,Chip-Seq and downstream analysis.

7. Knowledge in WGS ,WES, Targeted re-sequencing,GWAS and population genomics will be preferred.

8. Must have experience working on opensource software/Framework and commercial software for NGS data analysis and reporting.

9. Should be aware of handling big data and guiding team members on multiple projects simultaneously.

10. Should have experience coordinating with different groups of clinical research scientist for various project requirements.

11. Ability to work as team as well as independently with minimal support.

More at http://www.ocimumbio.com/careers1/

Liftoff: an accurate tool that maps annotations in GFF or GTF between assemblies

Jit — Tue, 30 Jun 2020 21:40:52 -0500

Liftoff, an accurate tool that maps annotations in GFF or GTF between assemblies of the same, or closely-related species. Unlike current coordinate lift-over tools which require a pre-generated “chain” file as input, Liftoff is a standalone tool that takes two genome assemblies and a reference annotation as input and outputs an annotation of the target genome.

Address of the bookmark: https://github.com/agshumate/Liftoff

A 3D Map of the Human Genome

Fri, 12 Dec 2014 22:27:55 -0600

Suhas Rao and Miriam Huntley (of the Aiden Lab) describe a 3D map of the human genome at kilobase resolution, revealing the principles of chromatin looping. Guest Origami Folding: Sarah Nyquist. Suhas S.P. Rao*, Miriam H. Huntley*, Neva C. Durand, Elena K. Stamenova, Ivan D. Bochkov, James T. Robinson, Adrian L. Sanborn, Ido Machol, Arina D. Omer, Eric S. Lander, Erez Lieberman Aiden. (2014). A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping. Cell.