MitoHiFi was first developed to assemble the mitogenomes for a wide range of species in the Darwin Tree of Life Project (DToL)

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-023-05385-y 

Address of the bookmark: https://github.com/marcelauliano/MitoHiFi

No.of Posts:01 (SC)

Pay Scale:

Pay Band of Rs.15600-39100 + Rs.6000/- GP +NPA @ 25% of Basic Pay +Learning Resource Allowance @ Rs.20,000/-P.A.+ Conveyance Allowance @ Rs. 1650/-P.M.+ Academic Allowance @ Rs.2500/- P.M. and other admissible allowances.

Qualifications:

Area of Specialization:-

Bioinformatics/Computational/Biology/Genomics/ Proteomics/ Structural Biology

1. Postgraduate qualification, e.g. Master’s Degree in Biotechnology/Bioinformatics/ Biophysics.

2. A Doctorate Degree of recognized University/Institute in a basic or allied Medical Science subject e.g. Medical Biotechnology/Biophysics. Bioinformatics/X-ray Crystallography/

Immunology/Structural Biology etc

Experience:

1.Minimum three years teaching and/or research experience in a recognized medical/research Institution in an allied medical subject after obtaining doctorate degree and preferably in Medical

Molecular Biology/ Biophysics/Structural Biology/Genomics and Clinical Proteomics/Computational Biology.

2. Minimum two publication with atleast one in international journal and atleast one as first author

Desirable:-

Consistently excellent scholastic/academic record, demonstrated ability to write grant proposal/(s) successfully, Post Doctoral training in a frontier area of medical Bioinformatics Research and of direct relevance to clinical diagnosis or patient care (preferably from a recognized top-ranking medical institution abroad)

Send your applications to O/O, Deputy Registrar, Recruitment & Establishment Cell, University of Health Sciences, Rohtak by 08.7.2014

For more details,please visit website:http://pgimsrohtak.nic.in/2014%20AP%20Advt.pdf

• AssemblyMapper : reference-guided genome assembly
• GapFiller : long-reads based gap filling
• TeloExplorer : telomere identification
• CentroMiner : centromere candidate prediction

https://academic.oup.com/hr/article/10/8/uhad127/7197191?login=false 

Address of the bookmark: http://www.atcgn.com:8080/quarTeT/home.html

1.Stupid for biologist: Biology is so complex that it will make bioinformatician feel stupid. There are no any universal fixed rules; it can surprise you any time. So be nice to biologists who ask questions and resolve your biological puzzles. Sometime you will have no idea what the hell you were doing either.

2.Puzzling why: Do not hesitate to ask question. Especially. at the beginning of project you will have to ask a lot of questions. Instead of puzzling it out at end check out and clear your doubt even for a single error. It may can leads to wrong conclusion.

3.Running marathon: The most of the biological software’s documentation is always incomplete. In other word they are no more than 95 percent complete. Sometime a single problem can halt your entire project for months. Compilation and running the pipelines in tedious because almost all are interdependent and need proper configuration. I face the same kind of problem with Evolver :( …

4.Folders missing: The pipelines generate lots of data, and we keep them in several folders for future use. But sometime we delete them by mistake and move to recovery…

5.Digging deeper: Digging deeper is fruitful, but some time it can be catastrophic. You may get frustrated or direction less. So keep a biologist with you for rescue …. Sometime an expert computer programmer to handle your server. Remember, the server will always go down when you need it the most.

The most common frustrating  common line: Why do we do this again?

nf-core/mag v5 (https://github.com/nf-core/mag) addresses this challenge by extending its reproducible Nextflow-based workflow for modern genome-resolved metagenomics.

A key addition is support for long-read-only metagenomic assembly and bin refinement, enabling long-read data to be processed through an integrated workflow. The release also introduces five additional binning tools, providing complementary strategies for recovering genomes from complex microbial communities.

The workflow has also expanded beyond conventional bacterial and archaeal MAGs, with improved classification of viruses and eukaryotes, together with enhanced genome-quality assessment.

Conceptually, the workflow brings together:

Reads → QC → Assembly → Binning → Bin refinement → Taxonomic classification → MAG quality assessment

The real strength of nf-core/mag is not any single algorithm, but the integration and reproducibility of multiple tools within a standardized workflow. This is particularly important for large-scale metagenomic studies where software versions, parameters, databases and computational environments can strongly influence results.

After seven years of development involving multiple curator teams and the wider nf-core community, v5 demonstrates how community-driven workflow development can keep metagenomic analysis aligned with rapidly evolving sequencing technologies.

The future of genome-resolved metagenomics is not simply longer reads—it is better integration of assembly, binning, refinement and quality control within reproducible computational workflows.

Read the full paper in Bioinformatics https://academic.oup.com/bioinformatics/article/42/9/btag628/8770536?

Job Description: We are interested in finding an excellent postdoc with interests in protein functional annotation, machine learning and computer grids. The position is open for 3.5 years at the Université Pierre et Marie Curie, in the heart of paris.

Research topic: Protein function annotation, multiple probabilistic models, domain architecture, machine learning, combinatorial optimization, computer grid.

Title: A novel integrative platform for large scale protein annotation that exploits a multitude of diversified probabilistic models in several protein signature databases.

We propose a novel integrated approach for large scale protein annotation that will exploit an unprecedented amount of genomic data as well as sophisticated machine learning techniques and combinatorial optimization approaches taking advantages of High Performance Computing (HPC) environments. The idea is to uncover as much as possible the evolutionary processes of protein sequences that took place throughout the whole tree of life and that affected the evolution of a protein family. We have already demonstrated in a previous work that the problem of functional annotation is inherent to the ability of uncovering such paths. Now, we shall extend this approach to large scale genome annotation by considering 11 different protein databases, constituted by about 10^9 protein sequences, and by producing a large pool of diversified probabilistic models coding for about 10^7 evolutionary protein pathways. Such models will be used to search for specific domains in genomes to be annotated. Our previous methodology needs to be fundamentally improved to deal with this large amount of biological data. In this project, we shall work on the algorithms to reduce the space of models and the search complexity, and we shall implement some important algorithmic changes towards the realization of a powerful integrated annotation tool.

Where: This project is run on the Laboratoire de Biologie Computationnelle et Quantitative UMR7238 CNRS-UPMC – Analytical Genomics team, headed by A.Carbone. It is co-advised with Pierre-Henri Wuillemin, Laboratoire d’Informatique de Paris 6 – Equipe DECISION.

Start date: September 1st, 2014
Contact Person: Alessandra Carbone
Contact: alessandra.carbone@lip6.fr

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

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/

ROLLING ADVERTISEMENT NO. 01/2014(E-1)
ADVERTISEMENT FOR THE POSITIONS OF ASSISTANT PROFESSOR CANDIDATES CAN APPLY ANY TIME DURING THE YEAR.

IIT Delhi invites applications from qualified Indian Nationals, Persons of Indian Origin (PIOs) and Overseas Citizens of India (OCIs) for the following positions in the various Departments/Centres/Schools (in the fields
mentioned alongwith them):
Post Pay Band Assistant Professor and Assistant Professor (on Contract) Rs.15600-39100 (PB-3) (Minimum pay of Rs.30000/-)+ AGP Rs.8000/-

The following norms will be followed for fixing the basic pay + AGP for Assistant Professors appointed on
contract with Ph.D but experience of 3 years or less:-
Type Qualification & Experience on the date of joining
Assistant Professor (Contract) PB3 (Rs. 15,600-39,100).

MINIMUM QUALIFICATIONS AND EXPERIENCE:
Ph.D. with First class at the preceding degree or equivalent in the appropriate branch with very good academic record throughout. A minimum of three years industrial/research/teaching experience, excluding however, the experience gained while Pursuing Ph. D. The candidates should preferably be below
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(c) Other Foreign Nationals, in whose case, if selected, appointment will be on a contract basis for up to 5 (five) years subject to permission from the Govt. of India before he/she can join IIT Delhi.
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AMAR NATH & SHASHI KHOSLA SCHOOL OF INFORMATION TECHNOLOGY:
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