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/

Address of the bookmark: https://hpcugent.github.io/easybuild/

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

The program is written in Java in order to provide a graphical user interface that is portable across a variety of computer platforms; indeed its name stands for "Local Alignments with Java". Currently it exists in two forms, a stand-alone application and a web-based applet, with slightly different capabilities.

Address of the bookmark: http://www.bx.psu.edu/~ratan/

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.

More at http://sequenceserver.com.

Address of the bookmark: https://github.com/wurmlab/sequenceserver

TMAP is a fast and accurate alignment software for short and long nucleotide sequences produced by next-generation sequencing technologies.

• The latest TMAP is unsupported. To use a supported version, please see the TMAP version associated with a Torrent Suite release below.

• Get the latest source code:

  git clone git://github.com/iontorrent/TMAP.git
   cd TMAP
   git submodule init
   git submodule update

https://github.com/iontorrent/TS/tree/master/Analysis/TMAP

Address of the bookmark: https://github.com/iontorrent/TS/tree/master/Analysis/TMAP

 All the nodes in the tree are clickable. This displays various information and options:

• The species name (and the associated common name if there is one)
• The rank (kingdom, family, class, species...)
• Ability to go to the corresponding node/species on NCBI web site (displayed in a new window)
• Possibility to download the corresponding subtree in newick extended format
• Possibilty to get the whole lineage from the current node/tip to the root of the tree.

Address of the bookmark: http://lifemap-ncbi.univ-lyon1.fr/