BOL: Related items

NearHGT

Jit — Wed, 22 Jun 2016 05:41:57 -0500

Horizontal gene transfer (HGT), the transfer of genetic material between organisms, is crucial for genetic innovation and the evolution of genome architecture. Existing HGT detection algorithms rely on a strong phylogenetic signal distinguishing the transferred sequence from ancestral (vertically derived) genes in its recipient genome. Detecting HGT between closely related species or strains is challenging, as the phylogenetic signal is usually weak and the nucleotide composition is normally nearly identical. Nevertheless, there is a great importance in detecting HGT between congeneric species or strains, especially in clinical microbiology, where understanding the emergence of new virulent and drug-resistant strains is crucial, and often time-sensitive.

We developed a novel, self-contained technique named Near HGT, based on the synteny index, to measure the divergence of a gene from its native genomic environment and used it to identify candidate HGT events between closely related strains. The method confirms candidate transferred genes based on the constant relative mutability (CRM). Using CRM, the algorithm assigns a confidence score based on “unusual” sequence divergence. A gene exhibiting exceptional deviations according to both synteny and mutability criteria, is considered a validated HGT product. We first employed the technique to a set of three E. coli strains and detected several highly probable horizontally acquired genes. We then compared the method to existing HGT detection tools using a larger strain data set.

When combined with additional approaches our new algorithm provides richer picture and brings us closer to the goal of detecting all newly acquired genes in a particular strain.

Availability: The method is publicly available athttp://research.haifa.ac.il/~ssagi/software/nearHGT.zip

Address of the bookmark: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004408

PASA: Gene Structure Annotation and Analysis

biogeek — Tue, 26 Dec 2017 21:14:03 -0600

PASA, acronym for Program to Assemble Spliced Alignments, is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation consistent with the most recently available experimental sequence data. PASA also identifies and classifies all splicing variations supported by the transcript alignments.

Address of the bookmark: http://pasapipeline.github.io/

chromoMap-An R package for Interactive Visualization and Annotation of Chromosomes

Jit — Sat, 07 Sep 2019 10:45:31 -0500

chromoMap provides interactive, configurable and elegant graphics visualization of chromosomes or chromosomal regions allowing users to map chromosome elements (like genes,SNPs etc.) on the chromosome plot.Each chromosome is composed of loci(representing a specific range determined based on chromosome length) that, on hover, shows details about the annotations in that locus range. The plots can be saved as HTML documents that can be shared easily. In addition, you can include them in R Markdown or in R Shiny applications.

Some of the prominent features of the package are:

visualizing polyploidy simultaneously on the same plot.
annotating groups of elements as distinct colors.
creating chromosome heatmaps.
adjusting chromosome range or visualizing chromosome regions such as genes
adding labels to the plot
adding hyperlinks to each element

Address of the bookmark: https://cran.r-project.org/web/packages/chromoMap/vignettes/chromoMap.html

Advertisement for Junior Research Fellow(JRF) at School of Computational and Integrative Sciences Jawaharlal Nehru University

Thu, 14 Jul 2016 07:24:53 -0500

Advertisement for Junior Research Fellow(JRF) - (1)

Applications are invited for a post in DST, India funded Project entitled: "Positive and negative impacts of macromolecular crowding agents during target site location by DNA binding proteins – origin of optimal search at physiological ionic concentration (Reference Number: ECR/2016/000188) ''. The selected candidate will be appointed purely on temporary basis, initially for two years as a JRF that may be extended to one year of SRF based on the performance.

Position: Junior Research Fellow (1)

Qualifications & Experience: Candidate must have a consistently good academic record with at least 60% marks in all throughout and must have qualified NET/GATE.

Desirable: Basic knowledge in the field of biophysics, molecular simulations and computational biology are desirable.

Salary: Consolidated Rs. 25,000 per month.

Tenure: The project duration is for three years and the selected candidate would be appointed after an interview. Appointment will be purely on temporary basis as stipulated by the existing rules of the University.

Interested candidates need to send an application to the address mentioned below mentioning the name of the project and post applied for (on the cover of the envelope).

The applications along with CV should be mailed at the address given below. Name, address, contact number and e. mail address of two referees must be enclosed with the application. The last date for the application is July 31st 2016.

Dr. Arnab Bhattacharjee (Principal Investigator)
Assistant Professor
School of Computational and Integrative Sciences
Jawaharlal Nehru University
New Delhi-110067
E-mail: arnab@jnu.ac.in

Note: 1. Only shortlisted candidates will be communicated to appear in the interview at SCIS, JNU and no other communications in this regard will be entertained.

2. No TA/DA will be paid for appearing in interview.

Web Apollo: a web-based genomic annotation editing platform

Jit — Fri, 28 Jul 2017 04:48:17 -0500

Web Apollo is the first instantaneous, collaborative genomic annotation editor available on the web. One of the natural consequences following from current advances in sequencing technology is that there are more and more researchers sequencing new genomes. These researchers require tools to describe the functional features of their newly sequenced genomes. With Web Apollo researchers can use any of the common browsers (for example, Chrome or Firefox) to jointly analyze and precisely describe the features of a genome in real time, whether they are in the same room or working from opposite sides of the world.

Address of the bookmark: http://genomearchitect.github.io/

JRF Bioinformatics at IIT, Delhi

Mon, 25 Jul 2016 03:26:20 -0500

No. IITD/IRD/RP03017/4254/Advertisement No.: IITD/IRD/093/2016
JRF Bioinformatics job vacancies in Indian Institute of Technology Delhi (IIT Delhi)
Title : Elucidation of Pathologically Relevant miRNAs Responsible for Disease Progression and Resistance to Chemotherapy in Chronic Lymphocytic Leukemia (CLL) (RP03017)
Qualification : Candidates having first class B. Tech. / M.Sc. Degree or equivalent in Bioinformatics or Biotechnology with NET qualification. Desirable: Candidates having computer programming skills (C++, Python, Java, Web designing using Materialize frameworks, database management, offline software GUI development) with knowledge of Linux server environment and / or experience in next generation sequencing (NGS) data analysis, MD simulations will be preferred.
No. of Post : 01
Pay Scale : Rs.25,000/-
How to apply
Walk-in test / interview will be held on 04/08/2016, 03.00 p.m. at Committee Room No. 230, Block-I, Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi-110016.

More at http://ird.iitd.ac.in/sites/default/files/jobs/project/IITD-IRD-093-2016.pdf

bpRNA: large-scale automated annotation and analysis of RNA secondary structure

Rahul Nayak — Wed, 23 May 2018 03:24:33 -0500

bpRNA, a novel annotation tool capable of parsing RNA structures, including complex pseudoknot-containing RNAs, to yield an objective, precise, compact, unambiguous, easily-interpretable description of all loops, stems, and pseudoknots, along with the positions, sequence, and flanking base pairs of each such structural feature.

The bpRNA code is written in perl and requires the Graph perl module. Several additional scripts for analysis are included. The source code is available at http://github.com/hendrixlab/bpRNA.

Address of the bookmark: http://github.com/hendrixlab/bpRNA

EMBOSS Apps

Jit — Wed, 27 Jul 2016 06:00:41 -0500

The programs are listed in alphabetical order, Look at the individual applications or go to the GROUPS page to search by category.

EMBASSY applications are described in separate documentation for each package.

Applications in the current release

Address of the bookmark: http://emboss.sourceforge.net/apps/release/6.6/emboss/apps/

KOALA: KEGG's internal annotation tool for K number assignment of KEGG GENES using SSEARCH computation

Abhimanyu Singh — Wed, 12 Dec 2018 09:16:55 -0600

KOALA (KEGG Orthology And Links Annotation) is KEGG's internal annotation tool for K number assignment of KEGG GENES using SSEARCH computation. BlastKOALA and GhostKOALA assign K numbers to the user's sequence data by BLAST and GHOSTX searches, respectively, against a nonredundant set of KEGG GENES. Annotate Sequence in KEGG Mapper and Pathogen Checker in KEGG Pathogen are special interfaces to the BlastKOALA server and can be executed in an interactive mode. See Step-by-step Instructions.

Reference: Kanehisa, M., Sato, Y., and Morishima, K. (2016) BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J. Mol. Biol. 428, 726-731. [pubmed] [pdf]

Address of the bookmark: https://www.kegg.jp/blastkoala/

SRF and JRF Bioinformatics at Tezpur University, Napaam

Wed, 03 Aug 2016 03:47:38 -0500

Applications are invited for the following temporary positions unde MHRD sponsored Centre of Excellence
in the Department of Computer Science and Engineering (CSE), Tezpur University

Qualification
and Experience : Senior Research Fellow (SRF) and JRF : First Class in M.E/M.Tech in CSE/IT/ECE with research
experience in relevant fields of research (Candidates having valid GATE/NET Score would be preferred).

Fellowship: Rs. 18,000/- per month (fixed)

Duration : 2 (Two) years and may be extended
depending on status of the project

Age Limit: Candidates should not be more than 32 years of
age in case of SRF and 28 years of age in case of JRF and TA. Upper age limit may be relaxed up to 5
years in the case of candidate belonging to SC/ ST/ OBC/ Women/ Differently abled.

How to Apply:
Interested candidates may send their application on plain paper by post along with his/her educational
qualifications, research experience certificates (for SRF), 02 copies of recent passport/stamp size photographs
and contact phone number to Professor D.K Bhattacharyya, Principal Investigator, Department of Computer
Science & Engineering, Tezpur University, Napaam – 784 028, or mail it to dkb@tezu.ernet.in
(or to smh@tezu.ernet.in) within 15 days of publication of this advertisement.

No TA/DA shall
be paid for attending the interview.

For more details: http://www.tezu.ernet.in/ProjectWalkin/Advt-DoRD-CSE-DKB-20-225-6779-A.pdf