BOL: Related items

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/

NGS Online Training

Sat, 27 Sep 2014 07:42:29 -0500

ArrayGen Technologies announces to provide online NGS training through out the globe. Now analyze your own NGS datasets from anywhere.For more information contact us at training@arraygen.com

Please visit our site at www.arraygen.com

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/

JRF in Bioinformatics @ INMAS, DRDO,Delhi

Wed, 01 Oct 2014 07:01:07 -0500

Institute of Nuclear Medicine and Allied Sciences (INMAS), Delhi under the aegis of Defence Research and Development Organisation (DRDO), is engaged in research and developmental work in radiation sciences, Neuro-Computing and Medical Image Processing. INMAS is looking for meritorious young researchers for pursuing research in the frontier areas at INMAS. The Institute invites applications from young and meritorious Indian nationals who are creative, have passion and desire to pursue R&D in frontier areas. INMAS possesses ambience of a research cum academic institute coupled with an advanced R&D infrastructure in a mission mode. It provides the best infrastructure, motivation and personality development prospects for talented students, dreaming of unparalleled success in their professional endeavors. INMAS provides state of the art research facilities for undertaking pioneering research with defence applications.

JRF (Maximum Tenure‐ Five Years: 2yrs as JRF and 3yrs as SRF)
A first class Master’s Degree in Bioinformatics (likely 2 posts)
Around Rs 16,000/ Plus 30% HRA (as per rules of funding agency)

Applications are invited from candidates possessing the above qualifications. The upper age limit is as on the last date for receipt of application. (5 years relaxation to SC/ST candidates, 3 years to OBC candidates, and other entitled categories as per Govt rules). Actual No. of vacancies may vary.

Application form can be download from the website www.drdo.gov.in and E Mailed to inmashrd@gmail.com.
Last date to apply by email is 1700 hrs on 15 Oct 2014
Incomplete applications are liable to be rejected.
Confirmation will be sent to short-listed candidates through email only
Antecedents of selected candidates will be verified.
Written Test will be conducted from 0930-1030 hrs. Latecomers will not be considered.
Candidates will be required to produce certificates/testimonials in original at the time of interview.
It may please be noted that offer of Fellowship does not confer on fellows any right for absorption in DRDO.
Candidates should carry photocopy of Application form sent by email with them.
No TA/DA will be paid for attending interview & on joining.
Last date to apply by email is 1700 hrs on 15 Oct 2014

More at http://drdo.gov.in/drdo/English/jrf29092014.pdf
http://drdo.gov.in/drdo/English/index.jsp?pg=inmas29092014.jsp

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

Internship Program for Bioinformatics / Biotechnology Professionals (No. Of Vacancy: 2)

Wed, 08 Oct 2014 01:10:08 -0500

ArrayGen is offering an Internship Program for Post graduate Bioinformatics / Biotechnology students and professionals. ArrayGen Technologies provide an excellent opportunity to gain research experience and explore if a scientific career is right for you. Currently we offer positions to outstanding students interested in Next Generation Sequencing (NGS) data analysis. Applications are accepted throughout the year. Accepted students will be listed on web with their schedules. Accepted students can attend our future workshops and trainings freely at the specified venue.

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

How far can bioinformatics go creating organisms used for testing?

Fri, 17 Oct 2014 02:08:16 -0500

"I think you can get very far on a technical level. The problem is that a human body is more complex than just one cell." ... "At some point we still need clinical tests on animals and humans before we use it for real treatment. But we will likely be able to remove 99 % of animal tests in the future." Erik Lindahl, Professor of Theoretical and Computational Biophysics at KTH Royal Institute of Technology is telling us about his work. From the episode "Science for life – mapping the building blocks of the human body". Watch the rest of the talk, and other talks at www.crosstalks.tv Crosstalks is an academic talkshow produced by KTH Royal Institute of Technology and Stockholm University.

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

Graduate research assistantships @ University of Nebraska-Lincoln (UNL)

Wed, 22 Oct 2014 10:05:31 -0500

Graduate research assistantships in quantitative genetics are available with Gota Morota in the Department of Animal Science at the University of Nebraska-Lincoln (UNL).

Current projects in the Morota lab include developing kernel-based whole-genome prediction and kernel-based genome-wide association models, polygenic modeling of binary traits, reexamining the results from quantitative genetics analysis in light of functional annotation, and extending kernel methods (such as GBLUP and RKHS) specifically tailored for diverse types of emerging omics data.

In addition, candidates will be expected to leverage opportunities to interact with faculty in animal genetics and biometrics at the UNL in the areas of bioinformatics, breeding, functional genomics, quantitative genetics, and molecular genetics.

Candidates should have a B.S. or M.S. degree in quantitative disciplines with strong background and interest in statistical computing.
The starting date is Fall 2015.
For more information about research in the Morota lab at the UNL, visit: http://www.morotalab.org

A letter of interest in the position, C.V., and contact information for
three references should be emailed to Gota Morota at .
Review of applications will begin immediately, and continue until the
positions are filled. Informal inquiries are also welcome.

Also, please see: http://animalscience.unl.edu/anscprospectivegraduatestudents