BOL: Related items

Synima: a Synteny imaging tool for annotated genome assemblies

Abhimanyu Singh — Tue, 30 Oct 2018 10:49:13 -0500

Synima written in Perl, which uses the graphical features of R. Synima takes orthologues computed from reciprocal best BLAST hits or OrthoMCL, and DAGchainer, and outputs an overview of genome-wide synteny in PDF. Each of these programs are included with the Synima package, and a pipeline for their use. Synima has a range of graphical parameters including size, colours, order, and labels, which are specified in a config file generated by the first run of Synima – and can be subsequently edited. Synima runs quickly on a command line to generate informative and publication quality figures. Synima is open source and freely available from https://github.com/rhysf/Synima under the MIT License.

Address of the bookmark: https://github.com/rhysf/Synima

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

ANItools web: a web tool for fast genome comparison within multiple bacterial strains

Jit — Wed, 14 Nov 2018 04:34:23 -0600

ANItools is a software package written by PERL scripts that can be run in a Linux/Unix system. If you want to compare bacterial genomes and calculate their average nucleotide identity (ANI), you could download and run this program directly. Or you could send us the genome sequence by email. Then we will do the analysis work for you.

https://academic.oup.com/database/article/doi/10.1093/database/baw084/2630454

Address of the bookmark: http://ani.mypathogen.cn/

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

Genobuntu: A software package containing more than 70 software and packages oriented towards NGS and genome assembly

BioStar — Tue, 11 Dec 2018 05:15:57 -0600

Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools.

Commonly used biological software and example script files for different assembly pipelines have also been provided, where the example script files can be updated to suit one’s experimental needs. Genobuntu attempts to reduce the amount of time and energy needed to build software workstations and it can also act as a good teaching source for a class room setting.

https://sourceforge.net/projects/genobuntu/

Address of the bookmark: https://sourceforge.net/projects/genobuntu/

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/

Hawkeye: an interactive visual analytics tool for genome assemblies

Abhimanyu Singh — Tue, 01 Jan 2019 11:56:17 -0600

Genome sequencing remains an inexact science, and genome sequences can contain significant errors if they are not carefully examined. Hawkeye is our new visual analytics tool for genome assemblies, designed to aid in identifying and correcting assembly errors. Users can analyze all levels of an assembly along with summary statistics and assembly metrics, and are guided by a ranking component towards likely mis-assemblies. Hawkeye is freely available and released as part of the open source AMOS project http://amos.sourceforge.net/hawkeye.

https://genomebiology.biomedcentral.com/articles/10.1186/gb-2007-8-3-r34

Address of the bookmark: http://amos.sourceforge.net/wiki/index.php?title=Hawkeye

LTR_retriever: accurately identifies and annotates LTR retrotransposons and use LAI to evaluates the continuity of genome assemblies.

Neel — Sun, 13 Jan 2019 07:14:31 -0600

LTR_retriever is a command line program (in Perl) for accurate identification of LTR retrotransposons (LTR-RTs) from outputs of LTRharvest, LTR_FINDER, and/or MGEScan-LTR and generating non-redundant LTR-RT library for genome annotations.

By default, the program will generate whole-genome LTR-RT annotation and the LTR Assembly Index (LAI) for evaluations of the assembly continuity of the input genome. Users can also run LAI separately (see Usage).

Address of the bookmark: https://github.com/oushujun/LTR_retriever

SAU Bioinformatics/Plant Biotech JRF Vacancy

Fri, 12 Dec 2014 21:27:12 -0600

Applications are invited for the post of Junior Research Fellow (JRF) to work on SERB, DST funded project entitled “Genome wide analysis of ascorbate oxidase multi-gene family and elucidating its role in negative regulation of stress response in rice” under the supervision of Dr. Ananda Mustafiz, Faculty of Life Sciences and Biotechnology, South Asian University.

Qualification: Highly motivated M.Sc. (Bioinformatics/ Biotechnology/ Life Sciences/ Botany/ Agriculture) students are encouraged to apply. Prior experience in Bioinformatics/Plant tissue culture work is preferable. Preferences would be given to DBT/ CSIR / UGC NET qualified students.

Application Procedure: A detailed CV indicating name, date of birth, address, contact number, e-mail address, educational qualifications, NET qualified or not, research experiences if any, should be e-mailed to This email address is being protected from spambots. You need JavaScript enabled to view it. on or before 24th December 2014.

Important Note: Only short listed candidates will be called for interview at Akbar Bhawan, Chanakyapuri, New Delhi. No TA/DA will be paid for attending the interview. SAU Selection Committee reserves the rights to relax any of the qualifications in case the candidate is found otherwise well qualified. The above- mentioned post is temporary and will be initially offered for a period of one year, which can be extended to one more year.

Advertisement: www.sau.ac.in/recruitment/vacancy.html

GMASS: a novel measure for genomeassembly structural similarity

Abhimanyu Singh — Sun, 14 Apr 2019 20:35:40 -0500

The GMASS score is a novel measure for representing structural similarity between two assemblies. It will contribute to the understanding of assembly output and developing de novo assemblers.

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2710-z

Address of the bookmark: http://bioinfo.konkuk.ac.kr/GMASS/htdocs/syncircos.php