https://www.pmgenomics.ca/hoffmanlab/

The Ensembl comparative genomics resources are one such reference set that facilitates comprehensive and reproducible analysis of chordate genome data. Ensembl computes pairwise and multiple whole-genome alignments from which large-scale synteny, per-base conservation scores and constrained elements are obtained. Gene alignments are used to define Ensembl Protein Families, GeneTrees and homologies for both protein-coding and non-coding RNA genes. These resources are updated frequently and have a consistent informatics infrastructure and data presentation across all supported species. Specialized web-based visualizations are also available including synteny displays, collapsible gene tree plots, a gene family locator and different alignment views. The Ensembl comparative genomics infrastructure is extensively reused for the analysis of non-vertebrate species by other projects including Ensembl Genomes and Gramene and much of the information here is relevant to these projects. The consistency of the annotation across species and the focus on vertebrates makes Ensembl an ideal system to perform and support vertebrate comparative genomic analyses. We use robust software and pipelines to produce reference comparative data and make it freely available.

Database URL: http://www.ensembl.org.

Address of the bookmark: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4761110/

More at http://busco.ezlab.org/

Address of the bookmark: http://busco.ezlab.org/

It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.

CrossMap is designed to liftover genome coordinates between assemblies. It’s not a program for aligning sequences to reference genome.

We do not recommend using CrossMap to convert genome coordinates between species.

More at http://crossmap.sourceforge.net/

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

HiCdat is easy-to-use and provides solutions starting from aligned reads up to in-depth analyses. Importantly, HiCdat is focussed on the analysis of larger structural features of chromosomes, their correlation to genomic and epigenomic features, and on comparative studies. It uses simple input and output formats and can therefore easily be integrated into existing workflows or combined with alternative tools.

More at http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0678-x

Address of the bookmark: https://github.com/MWSchmid/HiCdat

An NSF-funded REU to study Y-chromosome diversity and sex-biased dispersal in wild brown rats (Rattus norvegicus) is available in the Munshi-South Lab at Fordham University. Our lab is currently investigating rat evolution at scales ranging from landscape genetics of individual cities to global patterns of diversity. Development of resources for investigating Y-chromosome diversity will support many of these studies. The REU student will work with the lab to bioinformatically identify Y-chromosome SNPs, design SNPtype assays,
extract DNA, genotype samples, and analyze data.

We seek applicants interested in bioinformatics, evolutionary biology, and related disciplines. Applicants must have taken a college-level genetics course. This REU will require attention to detail, reliability, independence, and critical thinking.

This position is based at Fordham University's field station, the Louis Calder Center, in Armonk, NY. The Calder Center is located approximately 25 miles north of New York City in a protected woodland area. Housing
will be provided at the Calder Center for the duration of the REU (May 23 to Aug 12, 2016). Additionally, the student will receive a $6,000 stipend. The selected student will participate in professional development activities through the Calder Centers REU program, including presentation of results at a research colloquium at the end of the summer.

To apply, please send a one page personal statement about your scientific interests and how this REU will support your professional goals, unofficial transcripts including a list of Spring 2016 courses, and names of two professional references (including title, address, phone number, and email address) as a single pdf (with your last name in the file name) to Dr. Jason Munshi-South (jmunshisouth@fordham.edu).

Applications are due March 4th, 2016.

Jason Munshi-South

http://millslab.org/research.html

More at http://bioinform.github.io/breakseq2/

Download BreakSeq2

Latest version: https://github.com/bioinform/breakseq2/archive/2.2.tar.gz

For other versions, see "releases". https://github.com/bioinform/breakseq2/releases

Address of the bookmark: http://bioinform.github.io/breakseq2/

Essential qualification : Ph.D. in Bioinformatics/Biotechnology/Genetics/Computational Biology.Understanding of genomics data and advanced knowledge of Java, and C/C++ as the programming languages and the scripting language like perl and/or Python, SQL is preferred. Experience in High Performance Computing, data architecture, database development is desirable

Fellowship: Rs 35,000 /-

How to apply

Candidates are requested to send their CV, and a brief summary of research experience by e-mail careers.genetics@ktr.srmuniv.ac.in on or before 30/03/2016.

More at http://www.srmuniv.ac.in/jobs-applications-for-position-of-post-doctoral-fellow