BOL: Related items

320000 viruses in mammals yet to sequenced in future!!!

Rahul Agarwal — Tue, 03 Sep 2013 08:35:30 -0500

With current biological technique improvements, finally it is now possible to look at millions of unknown viruses at genomic level and understand the mechanism. According to available data, close to 70 per cent of emerging viral diseases such as HIV/AIDS, West Nile, Ebola, SARS, and influenza, are zoonoses - infections of animals that cross into humans.

To address the challenges of describing and estimating virodiversity, a team of investigators from Center for Infection and Immunity (CII) and EcoHealth Alliance began in jungles of Bangladesh - home to the flying fox.

Reference:

http://economictimes.indiatimes.com/news/news-by-industry/et-cetera/mammals-harbour-at-least-320000-new-viruses/articleshow/22253268.cms

http://www.bbc.co.uk/news/science-environment-23932400

methylKit

Jit — Fri, 03 Jun 2016 10:09:29 -0500

methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods such as Agilent SureSelect methyl-seq. In addition, methylKit can deal with base-pair resolution data for 5hmC obtained from Tab-seq or oxBS-seq. It can also handle whole-genome bisulfite sequencing data if proper input format is provided.

Address of the bookmark: https://github.com/al2na/methylKit

DNA RNA MEME

Neel — Thu, 28 Jan 2021 11:23:14 -0600

Explain the DNA and RNA with picture ...

LAPTI Lab

Thu, 12 Dec 2013 18:19:12 -0600

The main theme of our research is the understanding of how genetic information is decoded from DNA into RNA and proteins. Someone may find this topic a little strange and argue that we already know how this is happening.

Translational recoding.

RNA editing.

Evolution of the genetic code and translation.

More at http://lapti.ucc.ie/research.html

Lab page http://lapti.ucc.ie/index.html

RA at IISR Kozhikode

Thu, 15 May 2014 10:08:09 -0500

INDIAN INSTITUTE OF SPICES RESEARCH
(Indian Council of Agricultural Research)
Marikunnu P.O., Kozhikode – 673 012, Kerala

Walk- in- Test cum Interview (based on test) for the selection of Research Associate

under the scheme “Distributed Information Sub Centre –DISC” & Research Assistant under scheme “Phytophthora, Fusarium and Ralstonia diseases of Horticultural and Field Crops” will be held at this Institute as per details indicated below.

WALK -IN- TEST CUM INTERVIEW

Name of the post : Research Associate

Date of Interview : 21-05-2014 at 10.00 AM

No. of posts : One

Qualifications : a)Essential

Ph.D Degree in Bioinformatics OR : Masters degree in Bioinformatics with a minimum of
60% marks or equivalent OGPA with at least two years research experience as evidenced from fellowship/ associateship/training/published papers etc.

b)Desirable: Experience in NGS data analysis.

Emoluments : Rs. 23,000/- per month + HRA (Masters Degree Holders)

Rs. 24,000/- per month + HRA (Ph.D Degree Holders)

Upper age limit : 40 years for Men & 45 years for Women as on date of Interview (Upper Age limits are relaxable for SC, ST and OBC candidates as per Govt. of India norms (at present 5 years for SC/ST and 3 years for OBC)

Duration of Project : Till 31-03-2017.

Title of Assigment : Research Assistant (on contract basis)

No. of vacancy : One

Qualification : Essential : Post Graduation in Bioinformatics and Minimum one year experience in NGS data analysis

Desirable : Experience in Perl/Python/R

Remuneration : Rs. 20,000/- per month (consolidated)

Scope of work :

1. Analysis of different file formats and their conversions.

2. Assessing the quality of data and filtering of raw reads.
3. Assembling the raw reads-de novo as well as reference mapping.
4. Compression of aligned reads using Jam tools
5. RNA-seq. Analysis
6. Differential expression testing involving Normalization, Statistical testing, heat map generation & hierarchical clustering
7. Annotating the assembled genome and geneet testing and their validation
8. Metabolic pathway analysis
9. Comparative genomics
10. Setting up of genome browsers.

Period of Assigment : Initially for six months.

Date & Venue of Interview : 21-05-2014 at IISR, Kozhikode at 10.00 AM

More at http://www.spices.res.in/pdf/disc-advtmnt.pdf

Zhang Lab

Sun, 28 Dec 2014 12:43:08 -0600

We develop and use integrative bioinformatics approaches to extract biological meanings from experimental data and generate hypotheses for experimental validation. Please explore our website to learn more about our people and our research.

More at http://bioinfo.vanderbilt.edu/zhanglab/

BISR Jaipur

Tue, 07 Jul 2015 23:12:26 -0500

The Bioinformatics Centre at BISR has created an infrastructure for providing facilities to the users working in the field of Biological Sciences. The users of Rajasthan, Jaipur in particular, are using facilities available at the Bioinformatics Centre extensively. The centre has leased line Internet connection as well latest Bioinformatics software for sequence and structure analysis. The centre provides the following services:

Bioinformatics supports to researchers
Customized training in Bioinformatics for researchers and faculty members
Support in Installing, implementing and maintaining software on computer.
Create awareness for taking preventive measure against data security
Organize workshops on thrust ares of Bioinformatics
Research Training to students of Biotechnology and Bioinformatics

More at http://bioinfo.bisr.res.in/index.php

liftover

Jitendra Narayan — Mon, 08 Feb 2016 15:45:03 -0600

Convenient conversions between genome assemblie. The liftover package makes it easy to remap genomic coordinates to a different genome assembly.

More at https://github.com/aaronwolen/liftover

https://www.bioconductor.org/help/workflows/liftOver/

Address of the bookmark: https://github.com/aaronwolen/liftover

SATSUMA : Highly sensitive whole-genome synteny alignments.

Jit — Fri, 13 May 2016 05:25:26 -0500

Satsuma is a whole-genome synteny alignment program. It takes two genomes, computes alignments, and then keeps only the parts that are orthologous, i.e. following the conserved order and orientation of features, such as protein coding genes, non-coding genes, or neutral sequences. Satsuma does not require any pre-processing, such as repeat masking, since it will automatically detect ambiguous mappings.

Satsuma has parallelization built-in and is designed to run on multi-core architectures. The run-time for aligning two bird-size genomes (~1.2 Gb) is around two days on 24 CPUs.

You can find the manual here.
Download the latest source code from here.
Stable versions can also be downloaded from the Broad Institute's web site.

An incomplete list of questions and answers (yes, these have really been asked by our users! Please feel free to add your own by e-mailing us) is here.

If you use Satsuma in your research, please cite:
Grabherr, M. G., Russell, P., Meyer, M., Mauceli, E., Alföldi, J., Di Palma, F., & Lindblad-Toh, K. (2010). Genome-wide synteny through highly sensitive sequence alignment: Satsuma. Bioinformatics, 26(9), 1145-51.

Tutorial at http://evomics.org/learning/genomics/satsuma/

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

DIYA: a bacterial annotation pipeline for any genomics lab

Jit — Fri, 30 Jun 2017 08:48:26 -0500

DIY Genomics is an open source bioinformatics consortium intended to bring a collection of tools and libraries into the hands of small scale genomics labs for the process of sequence assembly and annotation. Projects include DIYA, MGAP, CRISPR, and DIYGV

http://gmod.org/wiki/Diya

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