BOL: Related items

Mugsy: multiple whole genome alignment tool

Jit — Fri, 08 Dec 2017 17:41:14 -0600

Mugsy is a multiple whole genome aligner. Mugsy uses Nucmer for pairwise alignment, a custom graph based segmentation procedure for identifying collinear regions, and the segment-based progressive multiple alignment strategy from Seqan::TCoffee. Mugsy accepts draft genomes in the form of multi-FASTA files and does not require a reference genome.

To cite Mugsy, use:

Angiuoli SV and Salzberg SL. Mugsy: Fast multiple alignment of closely related whole genomes.Bioinformatics 2011 27(3):334-4

Address of the bookmark: http://mugsy.sourceforge.net/

Walk in for Research Asst & Programmer Enterovirus Research Centre Mumbai - India

Tue, 14 Apr 2015 12:36:51 -0500

Enterovirus Research Centre Mumbai Jobs 2015 –

Walk in for Research Asst & Programmer Posts: Enterovirus Research Centre, Mumbai, Indian Council of Medical Research has issued notification for the recruitment of Research Asst & Programmer vacancies on temporary basis for the project entitled “An Atlas of Non-Polio Enterovirus Types Isolated from Cases of Acute Flaccid Paralysis in India”. Eligible candidates may walk in on 20-04-2015 from 10:00 AM to 12:00 Noon. Other details like age limit, educational qualification, how to apply are given below…

Enterovirus Research Centre Mumbai Vacancy Details:
Total No. of Posts: 04
Name of the Posts:
1. Research Assistant: 03 Posts
2. Programmer: 01 Post

Age Limit: Candidates age should below 28 years. Age relaxations are applicable as per rules.

Educational Qualification: Candidates should have M.Sc (1st Class) in Microbiology/ Bioinformatics/ Biotechnology/ Life Science for post 1, BE/ B.Tech/ MCA for post 2.

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

How to Apply: Eligible candidates may attend for interview along with original certificates, CV, attested copies of relevant certificates, one recent passport size photograph duly affixed on right side of application at Enterovirus Research Centre, Mumbai, Indian Council of Medical Research, Haffkine Institute Cmpound, Acharya Donde Marg, Parel, Mumbai-400012 on 20-04-2015 from 10:00 AM to 12:00 Noon.

Important Dates:
Date & Time of Interview: 20-04-2015 from 10:00 AM to 12:00 Noon.
Registration Time: 12:00 Noon.

GPOPSIM: a simulation tool for whole-genome genetic data

Jit — Wed, 17 Jan 2018 03:47:46 -0600

GPOPSIM is a simulation tool for pedigree, phenotypes, and genomic data, with a variety of population and genome structures and trait genetic architectures. It provides flexible parameter settings for a wide discipline of users, especially can simulate multiple genetically correlated traits with desired genetic parameters and underlying genetic architectures.

Address of the bookmark: https://github.com/SCAU-AnimalGenetics/GPOPSIM

BINC Sample Question Paper !!!

Jitendra Narayan — Thu, 16 Apr 2015 09:15:09 -0500

BINC sample question paper round THREE ...

%MinMax: A versatile tool for calculating and comparing synonymous codon usage and its impact on protein folding.

Surabhi Chaudhary — Thu, 24 May 2018 02:53:31 -0500

%MM calculates whether a given gene sequence encodes amino acids using the most common codons possible, the least common codons possible, or (most typically) some combination of these extremes. See our PLoS ONE paper for more details on how the %MinMax algorithm works. %MinMax results are averaged over an 18-codon sliding window; hence the result for "codon window = 1" is the average codon usage for codons 1-18, codon window 2 = codons 2-19, etc.

Address of the bookmark: http://www.codons.org/

Senior Research Fellow (SRF) Bioinformatics at Central Institute for Research on Buffaloes

Sat, 18 Apr 2015 04:30:47 -0500

Senior Research Fellow (SRF) Bioinformatics at Central Institute for Research on Buffaloes
Address: Central Institute for Research on Buffaloes, Sirsa Road, Hisar
State: Haryana
Pay Scale: Post Graduate in subjects other than Veterinary Science Rs. 16000/- per month for 1st and 2nd year and Rs. 18000/- per month for 3rd year. Post Graduate in Veterinary Science Rs. 18000/- per month for 1st and 2nd Year and Rs. 20000/- per month for 3rd year.
Educational Requirements: Master’s degree in biotechnology/animal biotechnology, veterinary/animal biochemistry, veterinary microbiology or veterinary/animal physiology/Nano Technology/Bioinformatics or related area.
Qualifications: Ph.D in relevant field/experience of working in any research project
Details will be available at: http://www.cirb.res.in/attachments/195_Walk-in-Interview%20for%20Senior%20Research%20Fellow%20%28SRF%29%20%28On%20Dated%2020.4.2015%29.pdf
How To Apply: Interested candidates who fulfill the above conditions should report for interview with a copy of their bio-data, photocopy and original certificates and testimonials, other related material i.e. reports, documents, articles, etc., if any.
Date & Time of Interview: 20.04.2015 at 11.00 hrs
Venue: CIRB, Hisar

EAGLER: a scaffolding tool for long reads.

Jit — Mon, 04 Jun 2018 05:26:03 -0500

EAGLER is a scaffolding tool for long reads. The scaffolder takes as input a draft genome created by any NGS assembler and a set of long reads. The long reads are used to extend the contigs present in the NGS draft and possibly join overlapping contigs. EAGLER supports both PacBio and Oxford Nanopore reads.

The tool should be compatible with most UNIX flavors and has been successfully tested on the following operating systems:

Mac OS X 10.11.1
Mac OS X 10.10.3
Ubuntu 14.04 LTS

https://bib.irb.hr/datoteka/844447.Diplomski_2015_Luka_terbi.pdf

Address of the bookmark: https://github.com/mculinovic/EAGLER

Savitribai Phule Pune University Recruitment for 04 JRF Post in April 2015

Mon, 27 Apr 2015 20:28:59 -0500

Savitribai Phule Pune University announced application for recruitment to the post of Junior Research Fellow. The candidates for the post can apply through prescribed format before 10 May 2015.
Description:

Important Date & Details

Closing Date for Registration: 10 May 2015

Details of Post

Name of Post: Junior Research Fellow- 04 Posts

Pay Scale: Rs. 12,000 or 16,00+ HRA Post Graduate degree with NET (16,000+HRA) Post Graduate Degree (12,000+HRA)

Eligibility Criteria: M.Sc. in Microbiology/Marine Microbiology/ Marine Biotechnology/Biotechnology/Bioinformatics/Zoology or equivalent degree with minimum 60% marks or equivalent grade

Age Limit- Not more than 28 years

Organisation Name: Savitribai Phule Pune University
Eligibility for the post:

Selection Procedure: The selection procedure is through personal interview. No TA/DA will be paid for appearing in the interview.

How to Apply: The candidates may send their application along with CV to the Head Department of Zoology, Savitribai Phule University on or before 10 May 2015.

mScaffolder: A comparative genome scaffolding tool

Jit — Fri, 15 Jun 2018 04:48:01 -0500

A comparative genome scaffolding tool based on MUMmer

mScaffolder scaffolds a genome using an existing high quality genome as the reference. It aligns the two genomes using nucmer utility from MUMmer and then orders and orients the contigs of the candidate genome guided by their alignments to the reference genome. Please send your questions and comments to mchakrab@uci.edu.

Citation https://www.nature.com/articles/s41588-017-0010-y

Address of the bookmark: https://github.com/mahulchak/mscaffolder

FMLRC: a long-read error correction tool using the multi-string Burrows Wheeler Transform

Neel — Fri, 10 Aug 2018 13:29:28 -0500

FMLRC, or FM-index Long Read Corrector, is a tool for performing hybrid correction of long read sequencing using the BWT and FM-index of short-read sequencing data. Given a BWT of the short-read sequencing data, FMLRC will build an FM-index and use that as an implicit de Bruijn graph. Each long read is then corrected independently by identifying low frequency k-mers in the long read and replacing them with the closest matching high frequency k-mers in the implicit de Bruijn graph. In contrast to other de Bruijn graph based implementations, FMLRC is not restricted to a particular k-mer size and instead uses a two pass method with both a short "k-mer" and a longer "K-mer". This allows FMLRC to correct through low complexity regions that are computational difficult for short k-mers.

Address of the bookmark: https://github.com/holtjma/fmlrc