BOL: Related items

320000 viruses in mammals yet to sequenced in future!!!

Rahul Agarwal — Tue, 03 Sep 2013 08:35:30 -0500

With current biological technique improvements, finally it is now possible to look at millions of unknown viruses at genomic level and understand the mechanism. According to available data, close to 70 per cent of emerging viral diseases such as HIV/AIDS, West Nile, Ebola, SARS, and influenza, are zoonoses - infections of animals that cross into humans.

To address the challenges of describing and estimating virodiversity, a team of investigators from Center for Infection and Immunity (CII) and EcoHealth Alliance began in jungles of Bangladesh - home to the flying fox.

Reference:

http://economictimes.indiatimes.com/news/news-by-industry/et-cetera/mammals-harbour-at-least-320000-new-viruses/articleshow/22253268.cms

http://www.bbc.co.uk/news/science-environment-23932400

Bioinformatics JRF/SRF position at NII

Sun, 25 May 2014 16:54:04 -0500

NATIONAL INSTITUTE OF IMMUNOLOGY, NEW DELHI-110067

Applications are invited for the position of Senior Research Fellow for the following time-bound sponsored project as per the details given below:

1. BTIS project on, “Bioinformatics Center-National Infrastructural Facility in the Area of Immunology” funded by DBT

Senior Research Fellow (P) (One Position only)

Dr. Debasisa Mohanty
Staff Scientist-VI
deb@nii.res.in

Qualifications: M.Sc in Biological Sciences or Biotechnology with at least 04 years of Research experience in Bioinformatics or computational Biology after the master’s degree is essential.

Emoluments: The selected candidates will draw consolidated emoluments as per Institute Rules, depending upon qualifications & experience

Rs. 18,000/- per month consolidated plus 30% HRA if Leading to Ph.D/NET/GATE Qualified otherwise Rs. 14,000/- per month + 30% HRA.

Job description: The candidate should be well versed in programming in PERL/C++/HTML/CGI, web server and portal development, computational analysis of
protein structure & function, molecular dynamics simulations and use of high performance computing systems.

GENERAL TERMS AND CONDITIONS:-

1. The candidates selected for the above posts will be on contract for one year or duration of the project whichever is shorter, at a time.
2. No hostel/ housing facility will be provided.
3. Number of posts may vary and shall be need based. Advertisement is no commitment.
4. Applicants may clearly mention the category they belong to i.e. SC/ST/OBC/PH and attach documentary proof of the same.
5. No TA/DA will be paid for attending the interview, if called for.
6. Apart from sending application in the prescribed format given below, candidates should send complete Curriculum Vitae along with the names of three referees. Curriculum Vitae should contain details of the experimental expertise.

HOW TO APPLY Interested candidates may apply directly, STRICTLY IN THE PRESCRIBED FORMAT GIVEN BELOW, through e-mail, to the Investigator of the project, clearly indicating the name of the project along with their complete C.V., e-mail id, fax numbers, telephone numbers. Only Short listed candidates will be called for interview and they required to submit attested copies of all their certificates and a Demand Draft of Rs 100/- drawn on Canara Bank or Indian Bank payable at Delhi/New Delhi in favour of the Director, NII (SC / ST and PH candidates are exempted subject to submission of documentary proof), at the time of interview.

LAST DATE OF RECEIPT OF APPLICATIONS: 06th June, 2014

www1.nii.res.in/sites/default/files/projectappointment-Dr.Mohanty-6June2014.pdf

Tools to detect synteny blocks regions among multiple genomes

Jitendra Narayan — Mon, 16 Sep 2013 17:12:02 -0500

The synteny block (which etymologically means “on the same ribbon”) is a collection of contiguous genes located on the same chromosome. These block regions have mostly been preserved by genome rearrangements, and so synteny blocks from two related species (e.g., humans and mice) will be roughly similar but flipped around on the respective genomes. Ovcharenko et. al. define it as ‘any conserved sequence blocks, regardless of whether it encompasses multiple genes, an area containing single genes, or areas devoid of known genes to be considers as synteny block as long as there is conservation at the sequence level. Today, however, biologists usually refer to synteny as the conservation of blocks of order within two sets of chromosomes that are being compared with each other. This concept can also be referred to as shared synteny. The NHBLI/NCBI Glossary define synteny as “Two genes which occur on the same chromosome are syntenic; however, syntenic genes may or may not be "linked."

Now a day, geneticists have developed a language of their own. They are pouring lots of money and energy to read the entire genomic text and understand the gods own code ATGC. It is somewhat fascinating, not only for geneticist but also for non-biologist to know that there are several conserved blocks in genome which remain conserved over hundreds of millions of years. There have been several researches on conserved blocks and non-conserved regions to understand the mechanism and importance of all these regions (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2675965/). The finding indicates conservation and rearrangements of certain evolutionary important genes play an important role in evolution/adaptive changes (http://www.nature.com/nature/journal/v491/n7424/abs/nature11622.html https://academic.oup.com/gbe/article/8/8/2442/2198198/Novel-Insights-into-Chromosome-Evolution-in-Birds , http://science.sciencemag.org/content/346/6215/1311).

But the puzzle remains open, how to correctly define the synteny (presence of two or more genes on the same chromosome) and conserved synteny (presence of two or more genes on chromosome of each of the two species) on several genomes.

Figure: Image generated with Evolution Highway (EH) tool http://eh-demo.ncsa.illinois.edu/

Keeping the new approach to define conserved synteny in mind there have been various algorithms developed to identify the conserved homologous synteny blocks (HSB) amongst species. Some of them which were commonly used for synteny detections are:

SyntenyTracker ( http://www-app.igb.uiuc.edu/labs/lewin/donthu/Synteny_assign/html/),

SyntenyTracker was shown to be an efficient and accurate automated tool for defining HSBs using datasets that may contain minor errors resulting from limitations in map construction methodologies.

CoGe (http://genomevolution.org/CoGe/SynFind.pl )

Satsuma (http://evomics.org/learning/genomics/satsuma/)

Cinteny (http://cinteny.cchmc.org/) ,

Cinteny server can be used for finding regions syntenic across multiple genomes and measuring the extent of genome rearrangement using reversal distance as a measure.

OrthoCluster (http://krono.act.uji.es/noticias/orthocluster-a-new-tool-for-mining-syntenic-blocks)

A new tool for mining syntenic blocks in comparative genomics

SynMap (http://genomevolution.org/wiki/index.php/SynMap),

SyMAP (http://www.symapdb.org/)

SyMAP (Synteny Mapping and Analysis Program) v4.0 is an automated system for identifying and displaying genome synteny alignments. The genomes may be represented by sequenced chromosomes (pseudomolecules), by draft sequence contigs, or by FPC physical maps (with BAC-end or marker sequence).

http://genomevolution.org/CoGe/SynMap.pl

RegionMiner (http://www.genomatix.de/online_help/help_regionminer/orthologous.html)

SyntenyMiner is being developed as an application to visualize and interrogate comparisons among multiple complete genome sequences. http://syntenyminer.sourceforge.net/

AutoGRAPH ( http://autograph.genouest.org/),

AutoGRAPH is an integrated web server for multi-species comparative genomic analysis. It is designed for constructing and visualizing synteny maps between two or three species, determination and display of macrosynteny and microsynteny relationships among species, and for highlighting evolutionary breakpoints.

SynChro(http://www.lgm.upmc.fr/CHROnicle/SynChro.html)

SynChro is a tool designed to define conserved synteny blocks. It reconstructs synteny blocks between pairwise comparison of multiple genomes. The reconstructed synteny blocks may overlap each other, be included in one another or duplicated due to micro-rearrangements.

SyntenyView ( http://www.cbs.dtu.dk/dtucourse/cookbooks/nikob/exercises/gf1_output_5.html),

Ensembl 'SyntenyView' shows conservation of large-scale gene order between species pairs. A brief summary of the calculation method appears at the bottom of this help page. The left of a 'SyntenyView' page displays a diagram of chromosomes with blocks of conserved synteny. The right of a page shows homology matches between individual genes within syntenic blocks.

SynBrowse ( http://www.synbrowse.org/),

SynBrowse (Synteny Browser) is a generic sequence comparison tool for visualizing genome alignments both within and between species. It is intended to help scientists study and analyze synteny, homologous genes and other conserved elements between sequences. This software is useful in studying genome duplication and evolution. It can also aid in identifying uncharacterized genes, putative regulatory elements and novel structural features of study species by comparing to a well annotated reference sequence, thus enabling genome curators to refine and edit annotations of species that have incomplete genome annotations.

Sibelia (http://arxiv.org/abs/1307.7941).

A comparative genomic tool: It assists biologists in analysing the genomic variations that correlate with pathogens, or the genomic changes that help microorganisms adapt in different environments. Sibelia will also be helpful for the evolutionary and genome rearrangement studies for multiple strains of microorganisms.

GSV (http://cas-bioinfo.cas.unt.edu/gsv/homepage.php)

Genome Synteny Viewer allows users to upload files which contain synteny regions between two or more genomes and interactively visualize the synteny between them. GSV also allows users to upload annotation files to visualize annotated regions in addition to synteny regions.

MicroSyn (http://www.lgm.upmc.fr/CHROnicle/SynChro.html)

MicroSyn software as a means of detecting microsynteny in adjacent genomic regions surrounding genes in gene families. MicroSyn searches for conserved, flanking colinear homologous gene pairs between two genomic fragments to determine the relationship between two members in a gene family.

SynOrth (http://synorth.genereg.net/)

Synorth [s n ôrth], named in combination of "synteny" and "ortholog", is designed for the study of evolutionary changes of genomic regulatory blocks (GRBs) in vertebrate genomes, and especially the changes following the whole-genome duplication in teleost fish, by tracing the ortholog genes gain and loss in ancient synteny blocks.

SyDiG (http://www.ncbi.nlm.nih.gov/pubmed/21441096)

Uncovering Synteny in Distant Genomes.

MapSynteny (http://www.automatizacionysistemas.com/download.html)

MapSynteny is a macro in MS Excel® able to create images to show the relationship between genetic maps and large sequences (scaffolds, chromosomes, BACs, etc.). Based on tab – delimited BLAST results and some formulas, a suitable image of syntenic relationships or physical mapping can be obtained. http://www.automatizacionysistemas.com/Poster_MapSynteny.pdf

One of the best synteny tutorial for beginer @ http://www.nature.com/scitable/topicpage/synteny-inferring-ancestral-genomes-44022

Reference:

http://www.nature.com/scitable/topicpage/synteny-inferring-ancestral-genomes-44022

http://www.nature.com/nature/journal/v491/n7424/full/nature11622.html

http://en.wikipedia.org/wiki/Synteny

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2675965/

Bioinformatics JRF vacancy at ICGEB, New Delhi

Wed, 23 Jul 2014 16:07:15 -0500

Junior Research Fellow for a DBT sponsored project entitled "Computational and experimental characterization of stage specific arginine methylation in P. falciparum proteome".

Candidates should have a 1st class MSc/MTech/BTech degree in Bioinformatics. Please send complete CV, quoting Application for RMETH-JRF-2014, by email to Dr. Dinesh Gupta: dinesh@icgeb.res.in

Closing date for applications: 6 August 2014

More at http://www.icgeb.org/tl_files/Vacancies/JRF.pdf

Bioinformatician duties and jobs !!!

Jitendra Narayan — Wed, 05 Mar 2014 14:32:26 -0600

Needle in a haystack ... ohh yes this is what bioinformatician do. We handle and analyse, Terabytes and Petabytes of genomic data on daily basis.

Linux Sort Commands for Bioinformatics

Rahul Nayak — Sat, 31 May 2014 15:41:16 -0500

Almost all the scripting languages such as Perl, Python etc have built-in sort, but unfortunately none of them are as flexible as sort command. But one when it come to space efficiency GNU sort stands at the top. It can sort a 20Gb file with less than 2Gb memory. It is not trivial to implement so powerful a sort by yourself.

sort a space-delimited file based on its first column, then the second if the first is the same, and so on:
sort input.txt

sort a huge file (GNU sort ONLY):
sort -S 1500M -t $HOME/tmp input.txt > sorted.txt

sort starting from the third column, skipping the first two columns:
sort +2 input.txt

sort the second column as numbers, descending order; if identical, sort the 3rd as strings, ascending order:
sort -k2,2nr -k3,3 input.txt

sort starting from the 4th character at column 2, as numbers:
sort -k2.4n input.txt

More Linxu sort command information

If you have any sort commands you'd like to share, please add them to our comments section below. For more help, you can also type:

man sort

or

sort --help

on your Unix/Linux system.

List of genome announcement, notes and reporting journals

Jit — Wed, 26 Jul 2017 08:01:38 -0500

Faced with an increasing number of articles describing DNA data and a need for more appropriate venues to present these data, some publishers and journals have responded by changing the structure and format of genome papers. Specifically, certain journals have started accepting very short manuscripts (500–1500 words) that present a new chromosome sequence, its GenBank accession number and little else. These pint-sized articles go by various names, such as genome reports, genome announcements, genome notes or genome letters, but will be referred to here broadly as genome reports. Their short length and minimal number (or complete absence) of figures, tables and article subheadings are a significant departure from long-form genome papers, which typically span 8–10 journal pages, contain many supporting items and have formal introduction, methods, results and discussion sections.

Following are the list of journals publishing pint-sized articles go by various names, such as genome reports, genome announcements, genome notes or genome letters, but will be referred to here broadly as genome reports.

1. Genome Announcements, American Society for Microbiology, Genome announcement, Impact factor 1.3, A 500-word report stating that the genome of a particular organism (prokaryote, eukaryote or virus) has been sequenced and providing a citable record of the corresponding GenBank submission. Must include abstract but no text headings can be used except for ‘Acknowledgments’ and ‘References’. Cannot include figures, tables or supplemental material to present data or analysis.

Link: https://mra.asm.org/

2. Genome Biology and Evolution, Oxford University Press, Genome report, Impact factor 4.2, Focused 1500-word papers (up to six tables or figures) that publish the main evolutionary message of new genome sequences as they become submitted to GenBank. May also contain specifically focused comparative analyses of previously published genomes that contain a substantial and novel insight of broadest evolutionary significance.

Link: https://academic.oup.com/gbe

3. Journal of Biotechnology, Elsevier, Genome announcement, Impact factor 2.9, A 500-word report announcing the availability of the completely annotated genome sequence of a biotechnologically relevant organism in the corresponding database (for eukaryotes, advanced draft genomes will also be considered). Articles can contain an Abstract, a brief report on the organism and its biotechnological relevance, a table summarizing the genome features, References and an Acknowledgement. Figures are generally not allowed.

Link: https://www.journals.elsevier.com/journal-of-biotechnology

4. Journal of Genomics, Ivyspring, Genome note, Impact factor N/A, A 1000-word report (10 reference limit; conclusions not permitted) describing novel data sets from high-throughput analysis of genotypes, phenotypes, gene expression, metabolomes, proteomes or genome assemblies.Standard metrics for data quality and the experimental design must be clearly reported.

Link: http://www.jgenomics.com/

5. Memórias do Instituto, Oswaldo Cruz Oswaldo Cruz Foundation, Genome announcement and highlight, Impact factor 1.6, Dedicated to publishing new genome information from eukaryote parasites, virus, bacteria and their respective vectors, as well as re-sequencing or comparative genome analyses. Should occupy no more than three printed pages including figures and/or tables.

Link: http://memorias.ioc.fiocruz.br/

6. Molecular Ecology Resources, Wiley, Genomic resources note, Impact factor 3.7, Short notes on newly assembled and annotated transcriptomes, genome fractions or whole genomes, and/or a library of SNP/SSR markers.Authors submit a short manuscript describing how the resource was developed and where the data can be accessed. Do not appear in journal as individual papers but are instead published as part of a summary article.

Link: https://onlinelibrary.wiley.com/journal/17550998

7. Standards in Genomic Science, BioMed Central (Springer), Short genome report, Impact factor 3.2, Short (∼500-word) article on newly sequenced genome. Article format must follow guidelines and template (available from journal Web site) put forward by the SGS. Any manuscripts not using template or that are missing key figures, tables and/or references (as per the guidelines) will be returned to authors. Rationale of the content model is to provide information that is consistently and uniformly presented for rapid and easy consumption by both human and machine readers.

Link: https://standardsingenomics.biomedcentral.com/

8. 3biotech, Springer, Short genome report, Impact factor 1.3, Short (∼500-word) article on newly sequenced genome. Article format must follow guidelines (available from journal Web site). Genome of a particular organism (prokaryote, eukaryote or virus) has been sequenced and providing a citable record of the corresponding GenBank submission.

Link: https://link.springer.com/journal/13205

Postdoc position at Centre Méditerranéen de Médecine Moléculaire - Nice - France

Wed, 04 Jun 2014 07:20:57 -0500

The research group of Dr. Michele Trabucchi at the Centre Méditerranéen de Médecine Moléculaire (C3M) at INSERM U1065 (University of Nice Sophia-Antipolis, France) is seeking candidates for a Postdoctoral fellow position to start on October 2014 for 3 years funded by FRM (Fondation pour la Recherche Médicale).
The broad interest of the lab is in understanding the expression control and function of small RNAs in activated myeloid cells (visit our webpage to check research interests and publications of the group : http://www.unice.fr/c3m/EN/Equipe10.html ).

The work will focus on the functional studies of small RNAs by using next-generation sequencing approaches.

Candidates should hold a Ph.D. degree and have strong background in bioinformatics.
The University of Nice Sophia-Antipolis provides a wide range of facilities and training essential for biomedical research.

Interested applicants should send a PDF with a cover letter stating research interests and qualifications, an updated CV, a summary of previous research experience and contact information for two references to Michele Trabucchi ( mtrabucchi@unice.fr )

Homepage: http://www.unice.fr/c3m/EN/Equipe10.html

Ten recommendations for creating usable bioinformatics command line software

RAJESH DETROJA — Sun, 08 Jun 2014 10:06:26 -0500

Bioinformatics software varies greatly in quality. In terms of usability, the command line interface is the first experience a user will have of a tool. Unfortunately, this is often also the last time a tool will be used. Here I present ten recommendations for command line software author’s tools to follow, which I believe would greatly improve the uptake and usability of their products, waste less user’s time, and improve the quality of scientific analyses.

Address of the bookmark: http://www.gigasciencejournal.com/content/2/1/15?utm_content=buffer25ee0&utm_medium=social&utm_source=twitter.com&utm_campaign=buffer

GMOL: An Interactive Tool for 3D Genome Structure Visualization

Jit — Wed, 21 Mar 2018 12:25:20 -0500

GMOL was developed based upon our multi-scale approach that allows a user to scale between six separate levels within the genome. With GMOL, a user can choose any unit at any scale and scale it up or down to visualize its structure and retrieve corresponding genome sequences.

Address of the bookmark: https://www.nature.com/articles/srep20802