The vital metaphase stage of cell division, when the sister chromatids migrated to the centre and lined up in a row, and pulled apart using attached microtubules in such a way that half the DNA ends up in each daughter cell. However, before the mitotic spindle‐mediated movement gets start and pulled DNA apart, the chromosomes are free to undergo recombination which involves the exchange of genetic material either between multiple chromosomes or between different regions of the same chromosome.

During recombination, the precise breakage of each strand, exchange between the strands, and sealing of the resulting recombined molecules happens. The “chromosomal breakpoints” refers to these places where they break. Mostly, this process occurs with a high degree of accuracy at high frequency in both eukaryotic and prokaryotic cells. But occasionally this “break and sealing/ break and reattach” process goes wrong and the reattachment happens in the wrong place which usually create disaster (with few exceptions).These chromosome disaster or abnormalities involve the gain, loss or rearrangement of visible amounts of genetic material during cell division. These abnormalities are of two type, the first one is numerical abnormalities  where severe disorders are caused by the loss or gain of whole chromosomes, which affect the copy number of hundreds or even thousands of genes. The second are structural abnormalities which can be unbalanced or balanced. The former are similar to numerical abnormalities in that genetic material is either gained or lost. The natural defects in chromosome segregation are linked to cancer and several genetic diseases (http://en.wikipedia.org/wiki/List_of_genetic_disorders). Therefore, the enzymes involved in regulating cell division are still the attractive drug targets for many diseases.

Apart from certain chromosome abnormalities, these “crossing over” of segments of maternal and paternal chromosomes to form hybrid chromosomes have some evolutionary importance and considered as a driver of genetic variation. Moreover, the chromosome breakage in evolution is considered to be non-random in nature(http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0020014). In addition the study of breakpoint regions and non-breakpoint (stable) regions of chromosomes indicates both the regions evolved in distinctly different ways ( http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2675965/). These breakage may lead to genetic diseases or participate to chromosomal rearranmgnets and contributed in development of new species.

I will try to explain the genome hotspots/Evolutionary Breakpoint Regions(EBRs)/fragile regions/weak fragments/  in my next blog.

Software for recombination detection:

RAT http://cbr.jic.ac.uk/dicks/software/RAT/

Breakpointer https://github.com/ruping/Breakpointer

DRP http://web.cbio.uct.ac.za/~darren/rdp.html

RB-finder http://www.ncbi.nlm.nih.gov/pubmed/18707535

LDhat2.0 http://ldhat.sourceforge.net/LDhat2.0/instructions.shtml

Reference:

http://www.nature.com/scitable/topicpage/genetic-recombination-514#

Image: Wikipedia , sciencelearn.org.nz

Recommended Articles:

http://www.friendshipcircle.org/blog/2012/05/22/13-chromosomal-disorders-youve-never-heard-of/

http://web.udl.es/usuaris/e4650869/docencia/segoncicle/genclin98/recursos_classe_%28pdf%29/revisionsPDF/chromosyndromes.pdf

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2775595/table/T2/

http://learn.genetics.utah.edu/content/disorders/chromosomal/

http://www.ncert.nic.in/html/learning_basket/biology/cc&cd.pdf

Orange Bioinformatics provides access to publicly available data, like GEO data sets, Biomart, GO, KEGG, Atlas, ArrayExpress, and PIPAx database. As for the analytics, there is gene selection, quality control, scoring distances between experiments with multiple factors. All features can be combined with powerful visualization, network exploration and data mining techniques from the Orange data mining framework.

Address of the bookmark: https://pypi.python.org/pypi/Orange-Bioinformatics/2.5.34

Responsibilities

Lead teams of scientists in structuring, prototyping, and executing large-scale bioinformatic and other analysis.
Develop novel bioinformatics, statistical, data processing, pathway, data mining and other algorithms to identify biological signals and their clinical correlates in broad kinds of individual and population data.
Develop novel platform-level analytical tools for sequence-based assays (assembly, annotation, variant calling and interpretation, phasing, genome structure, etc.), expression assays (RNAseq and microarray), proteomics, and metabolomics.
Develop statistical models that robustly correlate complex laboratory-derived information with phenotypic and clinical information.
Create scientifically rigorous visualizations, communications, and presentations of results.

Reference @ https://www.google.com/about/careers/search#!t=jo&jid=62095001

Address of the bookmark: http://www.vital-it.ch/

We work in a highly interdisciplinary environment at the interface of Computer Science and Biology. Since its inception, our lab has eagerly engaged in collaborative research partnerships with biological and experimental collaborators, facilitated by our affiliation with the Broad Institute and the Computational and Systems Biology initiative (CSBi) at MIT, our participation in the Epigenome Roadmap, ENCODE, and modENCODE consortia, and by several other ongoing collaborations at MIT, Harvard, and the Harvard Medical School affiliated hospitals.

http://compbio.mit.edu/

There are two options to run ShRec3D (on linuX only so far): the first one uses the Matlab complier runtime environment (MCR), the second one doesn't need any other library to be installed but only works with the latest versions of Linux (equivalent to Fedora 19 and above).

Address of the bookmark: https://sites.google.com/site/julienmozziconacci/#TOC-Downloads

Main research topics:
- Comparative and Population Genomics of Plant Symbionts
- Parasite Genome Evolution
- Experimental Evolution of Microbial Symbionts and Parasites
- Phylogenomics of Early Branching Fungi

More at http://corradilab.weebly.com/

Staff Scientists

Specialization: Applicant should have a Ph.D. with excellent academic credentials along with the track record of scientific productivity evidenced by publications/patents/products in the frontier areas of Plant Biology such as, Computational Biology, Genome Analysis and Molecular Mapping, Molecular Mechanism of Abiotic Stress Responses, Nutritional Genomics, Plant Development and Architecture, Plant Immunity, Molecular Breeding, Transgenics for crop improvement and other emerging areas based on plant genomics.

Remuneration: The length of experience and scientific accomplishments/quality of scientific productivity record will be major factors in deciding the level of appointment as Staff Scientist as well as starting salary in the Pay Bands of Rs 15,600-39,100 (with grade pay of 5400), and Rs 37,400-67,000 (with grade pay of 8,700 and 8,900) plus usual allowances admissible to the Central Government employees. However, NIPGR reserves the right to select candidates in the lower grade against the foregoing posts depending upon the qualifications and experience of the candidate. Reservation of posts shall be as per Govt. of India norms. Five posts (SC-2, ST-1, OBC-2) in the Pay Band of Rs 15,600-39,100 with Grade Pay of Rs 5400, are reserved.

More at http://www.nipgr.res.in/careers/vacancies_latest.php#

Apply online at http://www.nipgr.res.in/nipgr_recu/nipgr_recu.php

Form http://www.nipgr.res.in/files/careers/Application_Performa_2015.doc

This is an extensive tutorial to take you through the main features and gotchas of configuring GBrowse as a server. This tutorial assumes that you have successfully set up Perl, GD, BioPerl and the other GBrowse dependencies. If you haven't, please see the GBrowse HOWTO During most of the tutorial, we will be using the "in-memory" GBrowse database (no relational database required!) Later we will show how to set up a genome size database using the berkeleydb and MySQL adaptors.

More at http://elp.ucdavis.edu/tutorial/tutorial.html

Address of the bookmark: http://elp.ucdavis.edu/tutorial/tutorial.html

More at http://catchenlab.life.illinois.edu/stacks/

Address of the bookmark: http://catchenlab.life.illinois.edu/stacks/