Address of the bookmark: http://www.cytoscape.org/

School of Life Sciences

Department of Animal Biology

Applications are invited on a plane paper (along with copies of educational qualifications and experience) from eligible candidates for the selection of following position to work under a collaborative research project entitled “Development and application of high resolution genome conformation capture technology to investigate genome architecture in space and time” between University of Hyderabad and CR Rao advanced Institute of Mathematics, Statistics and Computer Sciences, sponsored by Department of Biotechnology, Government of India, New Delhi

Name and No. of positions JRF‐ONE

Emoluments for the position Rs. 25,000/p.m. + Eligible HRA

Qualifications MSc or M.Tech in any branch of biology/bioinformatics/computational biology/computer sciences/Mathematics/Physics

Duration Appointments are made initially for ONE year and can be extended further TWO years or until the duration of project

Our laboratory is interested in understanding signalling and spatiotemporal dynamics of 3‐Dimensional genome architecture and gene expression during embryonic stem cell differentiation by utilizing a combination of cellular, molecular genetics, Biochemical and computational tools in combination with next generation sequencing based chromatin structure analysing methods. Successful candidates shall pursue project related to either experimental or computational analysis of genome and Epigenomics data derived from human and mouse cells. Experience in Computational biology, bioinformatics, statistics, machine learning and algorithmic development is required. Knowledge of programming languages (e.g. C, C++, Perl, Python, Ruby etc.) and statistical framework (e.g. R, matlab, etc.) is preferable. Basic understanding of molecular biology will be an added advantage.

Interested candidates with the above mentioned qualification can send their curriculum vitae to Dr. K. Sreenivasulu, Department of Animal Biology, School of Life Sciences, South campus, University of Hyderabad or via email at positionssklab@gmail.com or svksl@uohyd.ernet.in.

Candidates with CSIR/UGC/ICMR/DBT/BINC qualifications if interested in above mentioned area of research are welcomed to approch principal investigator for a position leading to PhD. Last date for submission of applications is 17/06/2016. Eligible candidates will be called for an interview and they should carry all original certificates of the qualifying exam. No TA/ DA will be paid for attending the interview or at the time of joining the post.

Advertisement: http://www.uohyd.ac.in/images/recruitment/jrf_260516.pdf

More at http://www.ncbi.nlm.nih.gov/projects/HistoneDB2.0/index.fcgi/browse/

Address of the bookmark: http://www.ncbi.nlm.nih.gov/projects/HistoneDB2.0/index.fcgi/browse/

MutaBind guides you through this process, step by step, starting with selecting a protein complex and inputting PDB code or uploading PDB files. You can also retrieve results with a job ID number, view help documents, and review the MutaBind method and references.

More at http://www.ncbi.nlm.nih.gov/projects/mutabind/index.fcgi/

More at http://www.pondiuni.edu.in/news?quicktabs_2=5#quicktabs-2

Anvi’o is an analysis and visualization platform for ‘omics data.

Please find the methods paper here: https://peerj.com/articles/1319/

Anvi’o would not have been possible without the help of many people who directly or indirectly contributed to its development. Here is the acknowledgements section of our methods paper

An analysis and visualization platform for 'omics data http://merenlab.org/projects/anvio

Paper https://peerj.com/articles/1839/

Address of the bookmark: https://github.com/meren/anvio

LPI scores are inversely proportional to the phylogenetic distance between database match sequences and the query genome. These scores are useful not only for large-scalede novo predictions of horizontally transferred proteins, but can also serve as an independent quality control test for potential horizontal transfer candidates identified by alternative methods, especially those based on nucleic acid signatures. Candidates having high LPI scores are unlikely to have been horizontally transferred, since they are highly conserved among closely related organisms.

One unique and powerful feature of the DarkHorse HGT Candidate database is the opportunity to explore the phylogenetic background of potential HGT donors as well as recipients. The breadth of the database allows not only query sequences, but also their database match partners to be evaluated for sequence similarity or novelty compared to taxonomically related organisms.

DarkHorse is configurable for varying degrees of phylogenetic granularity and protein sequence conservation. Users should consult the references cited below for a complete explanation of parameter selection and result interpretation. A brief tutorial page is also available on-line.

Address of the bookmark: http://darkhorse.ucsd.edu/download.html

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

Wgsim is a small tool for simulating sequence reads from a reference genome. It is able to simulate diploid genomes with SNPs and insertion/deletion (INDEL) polymorphisms, and simulate reads with uniform substitution sequencing errors. It does not generate INDEL sequencing errors, but this can be partly compensated by simulating INDEL polymorphisms.

Wgsim outputs the simulated polymorphisms, and writes the true read coordinates as well as the number of polymorphisms and sequencing errors in read names. One can evaluate the accuracy of a mapper or a SNP caller with wgsim_eval.pl that comes with the package.

Address of the bookmark: https://github.com/lh3/wgsim

AVAILABILITY: QuIN’s web server is available at http://quin.jax.org QuIN is developed in Java and JavaScript, utilizing an Apache Tomcat web server and MySQL database and the source code is available under the GPLV3 license available on GitHub:https://github.com/UcarLab/QuIN/.

Address of the bookmark: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004809