Address of the bookmark: https://tritexassembly.bitbucket.io/

More at http://chibba.agtec.uga.edu/duplication/mcscan/

Address of the bookmark: http://chibba.agtec.uga.edu/duplication/mcscan/

The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotide or protein sequences, and to perform a wide variety of other motif-based analyses.

The MEME Suite supports motif-based analysis of DNA, RNA and protein sequences. It provides motif discovery algorithms using both probabilistic (MEME) and discrete models (MEME), which have complementary strengths. It also allows discovery of motifs with arbitrary insertions and deletions (GLAM2). In addition to motif discovery, the MEME Suite provides tools for scanning sequences for matches to motifs (FIMO, MAST and GLAM2Scan), scanning for clusters of motifs (MCAST), comparing motifs to known motifs (Tomtom), finding preferred spacings between motifs (SpaMo), predicting the biological roles of motifs (GOMo), measuring the positional enrichment of sequences for known motifs (CentriMo), and analyzing ChIP-seq and other large datasets (MEME-ChIP).

The MEME Suite is comprised of a collection of tools that work together, as shown below. Not all the tools are available as webservices, so to get the full power of the MEME Suite you will need to download and install a local copy of the software. To see what has changed recently you can peruse the release notes.

http://meme-suite.org/

Address of the bookmark: http://meme-suite.org/

Progressive Cactus is a whole-genome alignment package.

Requirements

• git
• gcc 4.2 or newer
• python 2.7
• wget
• 64bit processor and build environment
• 150GB+ of memory on at least one machine when aligning mammal-sized genomes; less memory is needed for smaller genomes.
• Parasol or SGE for cluster support.
• 750M disk space

Instructions

IMPORTANT NOTE: Progressive Cactus does not presently support installation into paths that contain spaces. Until this is resolved, you can use a softlink as a workaround: ln -s "path with spaces" "installation path without spaces"

In the parent directory of where you want Progressive Cactus installed:

git clone git://github.com/glennhickey/progressiveCactus.git
cd progressiveCactus
git pull
git submodule update --init
make

It is also convenient to add the location of progressiveCactus/bin to your PATH environment variable. In order to run the included tools (ex hal2maf) in the submodules/ directory structure, first source progressiveCactus/environment to load the installed environment.

If any errors occur during the build process, you are unlikely to be able to use the tool. Please submit a GitHub issue so we can help out: not only will you help yourself, but others who wish to use the tool as well.

Note that all dependencies are also built and included in the submodules/ directory. This increases the size and build time but greatly simplifies installation and version management. The installation does not create or modify any files outside the progressiveCactus/ directory.

Address of the bookmark: https://github.com/glennhickey/progressiveCactus

Positions available

Applications were invited from for the following posts in an industry sponsored project. The project entitled "OsHK3b technology and Know How", valid for a period upto February, 2018.

Post 3: Senior Research Fellow (Computational Biologist / Metabolic engineering)

Salary: As per DBT rule.

Duration: All the above posts are purely temporary and liable to be terminated at any time without prior notice or ceased/withdrawn by the funding agency.

Age limit: The upper age limit for SRF shall be 32 years, which is relaxed upto 5 years in the case of candidates belonging to Schedule Castes/Schedule Tribes, Women, Physically Handicapped and OBC applicants.

Essential Qualifications: Masters/B Tech/Mtech in Basic Sciences with at least 2yrs of research experience in Bioinformatics/Computational Biology related to Database /portal building & maintenance, high throughput data handling and analysis etc. For M.Sc/B.Tech, Published paper in peer-reviewed Journal and for M.Tech, thesis submission in computational biology is a must. Selection preference will be given to candidates with a good knowledge of Python and/or R. Knowledge of JAVA will also get a special consideration.

Desired Skills: Will be expected to manage ongoing research activities in the project, interact with Experimental group, manage the project data analysis, prepare file reports and associated project work etc. Familiarity with plant systems biology and genomics /metabolite resources related to plant metabolomics is desirable.

1. The post applied for must be clearly written on the Envelope containing the application
2. Applications received after last date shall not be entertained, School will not be responsible for any postal delay.
3. No application will be accepted via hand delivery or via e-mail. Please send printed & signed applications with detailed CV on or before 31st January, 2017 by post to the following address:

Prof. Ashwani Pareek
(Project Investigator)
Stress Physiology and Molecular Biology Laboratory (Room No-413),
School of Life Sciences,
Jawaharlal Nehru University,
New Delhi, India – 110067
Email: ashwanipareek@gmail.com

Pondicherry University, Puducherry has been identified as a nodal agency by the Department of Biotechnology, Govt. of India to coordinate this examination along with nine centres namely,

Pune University, Pune;

Anna University, Chennai;

Bose Institute, Kolkata;

Institute of Bioinformatics & Applied Biotechnology, Bangalore;

North-Eastern Hill University, Shillong, University of Hyderabad, Hyderabad;

University of Kerala, Thiruvananthapuram;

Jawaharlal Nehru University, New Delhi and

Assam Agricultural University, Guwahati. 

In the BINC 2015 and 2016 examination, 23 candidates and five candidates were certified respectively. DBT has agreed to fund Research fellowships for all the BINC qualified Indian nationals to pursue Ph.D. in Indian Institutes/Universities.

Note that the candidate must possess a postgraduate degree(or equivalent) & meet the criteria of the institutes/universities in order to avail research fellowship.

In addition, cash prize of Rs. 10,000/- will be awarded to the top 10 BINC qualifiers.

More at http://www.pondiuni.edu.in/exams/binc/

Address of the bookmark: http://www.ub.edu/dnasp/

Basic usage:

Rscript Ideoplot.R --heatmap hm.bed --annotate annotations.bed --out ideogram.pdf
-or-
Rscript Ideoplot.R --annotate annotations.bed

Options
  --ideobed, i      A bed file of reference contig lengths/chromosome names
  --heatmap, -h     Fill chromosomes with normalized heatmap
                   (described below)
  --annotate, -a    Add character annotations.
  --out, -o         PDF output name.
  --stripes, -s     Specify a file containing the layout of the
                    annotations (description below)
  --bars, -b        Add track annotations
  --reference, -f   Either hg19, or hg38
  --topdown, r      Flag, when set, flips the orientation (P arms
                    drawn on top).

Address of the bookmark: https://github.com/mchaisso/Ideoplot

This software distribution includes both the DAGchainer utility and a Java-based graphical interface that allows the inputs and outputs to be navigated and interrogated dynamically.

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

Applications are invited for:

Junior Research Fellow, in a DBT funded project, is available in Translational Health Group, ICGEB, New Delhi

Qualifications:

Education: M.Sc. (preferably in Biotechnology, Life Sciences or Zoology, Chemistry, Bioinformatics). Candidates with hands on experience on GC-MS data acquisition and analysis will be given preference. Bioinformatics expertise required.

Fellowship: As per DBT guidelines.

Tenure: The position is purely on temporary basis with an initial tenure of six months and based on satisfactory performance may continue until the completion of the project.

Closing date for applications: 04/03/2017

Please send a "TWO PAGE" CV by email to: th.icgeb@gmail.com on or before the last date.

Research Associate, in a DBT funded project, is available in Translational Health Group, ICGEB, New Delhi

Qualifications:

Education: Ph.D. (in Biology, Biotechnology, Chemistry, Bioinformatics). Candidates with hands on experience on GC-MS data acquisition and analysis will be given preference.

Fellowship: As per DBT guidelines.

Tenure: The position is purely on temporary basis with an initial tenure of six months and based on satisfactory performance may continue until the completion of the project.

Closing date for applications: 04/03/2017

Please send a "TWO PAGE" CV by email to: th.icgeb@gmail.com on or before the last date.