BOL: Related items

MGSE: Mapping-based Genome Size Estimation

Shruti Paniwala — Fri, 17 Jan 2020 02:11:43 -0600

MGSE can harness the power of files generated in genome sequencing projects to predict the genome size. Required are the FASTA file containing a high continuity assembly and a BAM file with all available reads mapped to this assembly. The script construct_cov_file.py (https://doi.org/10.1186/s12864-018-5360-z) allows the generation of a COV file based on the (sorted) BAM file (also possible via MGSE directly). Next, this COV file can be used by MGSE to calculate the coverage in provided reference regions and to calculate the total number of mapped bases. Both values are subjected to the genome size estimation. Providing accurate reference regions is crucial for this genome size estimation.

Address of the bookmark: https://github.com/bpucker/MGSE

Coding Ground

Jitendra Narayan — Tue, 17 Mar 2015 00:47:20 -0500

Online coding group for most of the programming languages.

Code in almost all popular languages using Coding Ground. Edit, compile, execute and share your projects, 100% cloud.

http://www.tutorialspoint.com/codingground.htm

Address of the bookmark: http://www.tutorialspoint.com/codingground.htm

U-Plot: Genome U-Plot sample implementation

Rahul Nayak — Tue, 03 Mar 2020 01:39:12 -0600

The Genome U-Plot is a JavaScript tool to visualize Chromosomal abnormalities in the Human Genome using a U-shape layout.

Address of the bookmark: https://github.com/gaitat/GenomeUPlot

Bioinformatics Project Assistant at NITW

Wed, 01 Apr 2015 01:43:27 -0500

NATIONAL INSTITUTE OF TECHNOLOGY WARANGAL – 506 004

DEPARTMENT OF BIOTECHNOLOGY

No. NITW/Bio/ Date: 30th March 2015

ADVERTISEMENT FOR PROJECT FELLOW (Research Staff)

Applications are invited for the post of Project Fellow (Research Staff) for the project entitled ‘Metagenome derived nitroreductases for degradation of nitro compounds’ sponsored by the Department of Science and Technology (DST-INSPIRE), Govt. of India.

Position: Project Fellow (1 No.)

Project Duration: 5 years

Note: The post is purely on temporary basis for a period one year and may be extendable till the end of the project based on the progress of the candidate.

Emoluments: Rs. 14,000/- per month (Consolidated) for first two years and Rs. 16,000/- per month (Consolidated) for next three years.

Essential Qualifications:

i) First class in M.Tech/M.S (Biotechnology/Industrial Biotechnology/Bioinformatics) or equivalent. Or

ii) First class in M.Sc. (Biotechnology/Bioinformatics/Biochemistry/ Microbiology/Molecular biology).

Desirable Qualification: Preference will be given to candidates who have cleared NET/GATE or having prior work experience in Molecular biology/Bioinformatics sequence analysis.

Interested candidates may submit their application in plain paper along with Curriculum Vitae and photocopies of certificates in support of educational/professional qualifications. Application should be sent in a closed cover with a superscription on the cover “Application for the post of project fellow (DST-INSPIRE)” on or before 20.04.2015 (Monday) via Post to the Principal Investigator. Eligible candidates will be intimated through e-mail and called for interview at the Department of Biotechnology, NIT, Warangal. No TA/DA will be paid for attending the interview. Dr. K. Divakar (Principal Investigator) DST-INSPIRE Faculty Department of Biotechnology National Institute of Technology Warangal – 506 004. Telangana, India. E-mail: divakar@nitw.ac.in; kdivak@gmail.com

Advertisement: http://www.nitw.ac.in/nitw/announcements/2015/Notification_Project_Fellow_DST_INSPIRE_Biotechnology_NITW.pdf

Genome assembly training tutorial at Galaxy !

Jit — Sun, 27 Dec 2020 05:25:45 -0600

In this tutorial we assemble and annotate the genome of E. coli strain C-1. This strain is routinely used in experimental evolution studies involving bacteriophages. For instance, now classic works by Holly Wichman and Jim Bull (Bull 1997, Bull 1998, Wichman 1999) have been performed using this strain and bacteriophage phiX174.

Address of the bookmark: https://training.galaxyproject.org/training-material/topics/assembly/tutorials/unicycler-assembly/tutorial.html

Bioinformatics RA at IVRI

Tue, 07 Apr 2015 03:10:53 -0500

A walk in interview is scheduled in the seminar hall of Veterinary Biotechnology Division of the institute on 9.04.15 at 10.30 am for the engagement of one Research associate (RA) in ICAR funded time bound project entitled “Centre for Agricultural bioinformatics (CABin)”.

The engagement is purely temporary on contractual basis and co-terminus with the project. There will be no provision of absorption of absorption/reemployment in IVRI/DBT on termination of the project.

No TA/DA will be provided for appearing in the interview and no separate letter will be issued.

A. Name tile of the project: “Centre for Agricultural bioinformatics (CABin)”.

B. Position/post to be filled: Research Associate (one)

C. Essential/Desirable qualifications:

•Essential: M.V.Sc./M.Tech./MSc Degree in Biotechnology/ Biochemistry/ Microbiology/Immunology/Bioinformatics/Genetics/Life Sciences or

Masters in Computer Application/ Masters in Computer science with first division.

• Desirable: Experience in cell culture, next generation sequencing, C++ and perl programming. NET/GATE qualified will be preferred.

• Experience : At least 2 years

D. Emoluments: Rs. 23000/- per month + 20% HRA

E. Age Limit: Maximum 40 years for men and 45 years for women

F. Duration of the project: Up to March 2017

G. Name of PI/Contact person: Dr. G.V.P.P.S. Ravi Kumar, Sr. Scientist, Division of Veterinary Biotechnology.

H. Address for correspondence: Dr. G.V.P.P.S. Ravi Kumar, Sr. Scientist, Computational Biology and Genomics facility,Division of Veterinary Biotechnology, I.V.R.I., Izatnagar – 243122

Advertisement: www.ivri.nic.in/jobs/WalkIn_interview_01042015.pdf

QuasiModo - Quasispecies Metric Determination on Omics

Neel — Sat, 26 Jun 2021 15:22:56 -0500

This repository contains the scripts and pipeline that reproduces the results of the HCMV benchmarking study. In this study we evaluated genome assemblers and variant callers on 10 in vitro generated, mixed strain HCMV sequence samples, each consisting of two lab strains in different abundance ratios. This tool can also be used to evaluate assemblies and variant calling results on other similar datasets.

https://academic.oup.com/bib/article/22/3/bbaa123/5868070

Address of the bookmark: https://github.com/hzi-bifo/Quasimodo

JRF Bioinformatics @ NATIONAL INSTITUTE OF IMMUNOLOGY NEW DELHI-110067

Fri, 17 Apr 2015 02:39:37 -0500

Applications are invited for the position of Junior Research Fellow (Project)/Senior Research Fellow (Project) for the following time-bound sponsored project as per the details given below:

1. “Development of bioinformatics methods for identifying novel secondary metabolites by genome mining” funded by DBT

JRF (P)/SRF (P) (One Position only)

Dr. Debasisa Mohanty Staff Scientist-VI deb@nii.res.in

Educational Qualifications: JRF (Project): M.Sc (Bioinformatics/ Biophysics/Biotechnology or any other stream of biological/physical sciences) or M.Tech. (Bioinformatics/Biotechnology/Computational Sciences) of M. Pharm.

SRF (Project): M.Sc (Bioinformatics/Biophysics/Biotechnology or any other stream of biological/physical sciences) or M.Tech. (Bioinformatics/Biotechnology/Computational Sciences) of M. Pharm with atleast 03 years of research experience.

Desirable Qualifications: Strong computer programming skills (in PERL/CGI/PHP or C++ or object oriented database management systems like MySQL etc or scripting languages under LINUX/UNIX environment) and sufficient experience in computational analysis of biological/biochemical data.

The candidates must highlight their experience in programming and database development in their CV. Job description: Computational analysis of genomes and development of bioinformatics tools and software’s for sequence and structure based analysis of biosynthetic pathways.

Emoluments: The selected candidates will draw consolidated emoluments as per Institute Rules, depending upon qualifications & experience JRF (Project): Rs. 12,000/- per month plus 30% HRA SRF (Project): Rs. 14,000/- per month plus 30% HRA (*Candidates possessing qualifications as per latest DST OM, will be given revised scales).

More at http://www1.nii.res.in/sites/default/files/projectappointments-Dr.DebasisaMohanty-30April2015.pdf

OGDRAW - Draw Organelle Genome Maps

Abhi — Tue, 05 Oct 2021 03:34:35 -0500

OrganellarGenomeDRAW converts annotations in the GenBank or EMBL/ENA format into graphical maps. The input has to be a GenBank or EMBL/ENA flat file wherase the output can vary among several types of files. The application is optimized to create detailed high-quality maps of organellar genomes (plastid and mitochondria). Nevertheless, you can upload most database entries.

Please take a look at our FAQ section and do not hesitate to report bugs or suggestions for improvements by email.

Address of the bookmark: https://chlorobox.mpimp-golm.mpg.de/OGDraw.html

IGIB Recruitment 2015 – Project Scientist

Tue, 14 Apr 2015 12:19:59 -0500

IGIB Recruitment 2015 – Project Scientist & SPF Posts: CSIR – Institute of Genomics & Integrative Biology (IGIB) has issued notification for the recruitment of Project Scientist, Sr Project Fellow vacancies on temporary basis for project entitled “Setting up of CSIR(unit)-TRISUTRA (Translational research and Innovative Science through Ayurgenomics)”. Eligible candidates may apply in prescribed application format on or before 23-04-2015. Other details like age limit, educational qualification, selection process & how to apply are given below…

IGIB Vacancy Details:
Total No. of Posts: 04
Name of the Posts:
1. Project Scientist (Biology): 02 Posts
2. Project Scientist (Bioinformatics): 01 Post
3. Sr Project Fellow (Ayurveda): 01 Post

Age Limit: Candidates age should be 35 years for post 1, 32 years for post 2

Educational Qualification: Candidates should have Ph.D/ Ph.D submitted in any branch of Biological Science/ Life Science for post 1, Ph.D/ Ph.D submitted in Bioinformatics for post 2, BAMS degree with one year internship for post 3.

Selection Process: Candidates will be selected based on their performance in interview.

How to Apply: Eligible candidates may send their application along with all relevant documents on or before 23-04-2015.

Important Dates:
Last Date for Receipt of Application for Post 1 & 2: 23-04-2015.
Date of Interview for Post 3: 27-04-2015.

For other details like pay scale, age relaxation, educational qualification, selection process, how to apply, etc., click on the link given below…

http://www.freejobalert.com/wp-content/uploads/2015/03/Notification-IGIB-Project-Scientist-SPF-Posts.pdf

http://www.igib.res.in/sites/default/files/27042015.pdf