More at https://pubmed.ncbi.nlm.nih.gov/34951622/

Address of the bookmark: https://github.com/EbmeyerSt/GEnView

Essential qualifications for JRF
: M. Sc. in Bioinformatics with experience in Proteomics, genomics and structural biology. Knowledge of programming language, pearl and database – HTML, CSS,php and Java script.
Essential qualifications for Research Associate:
MSc/MTech in Bioinformatics with three years experience or Ph.D in Bioinformatics with experience in proteomics, genomics and structural biology. Knowledge of programming language, perl and database
– HTML, CSS, Java script. NGS sequence assembly and analysis and algorithm designing.
Age limit : 35 years maximum (5 year relaxation for SC/ST and women candidates)
Emoluments:
JRF: 16,000 + 30% HRA
.
Res Assoc: Rs22,000 + 30% HRA
The post is purely temporary in nature and is co-terminus with the project. The appointment would be initially for one year and may be extended further upon satisfactory performance.
Interested candidates
should send the duly filled application forms (format in the following page ) so as to reach on or before 20.9.2014 along with all the relevant documents.

More at http://www.iari.res.in/files/JRF_RA-03092014-20140903-135319.pdf

In this post, we’ll explore the core methods used in comparative genomics, the questions they help answer, and how they’re shaping our understanding of life.

1. Whole-Genome Alignment
Whole-genome alignment involves mapping the entire genome of one species to another. Tools like MUMmer, MAUVE, and LASTZ perform large-scale sequence alignments to detect conserved regions, rearrangements, insertions, and deletions.

Use Case:
Comparing human and chimpanzee genomes to identify evolutionary conserved sequences (ECS) and regions of divergence.

Key Challenges:
Handling repetitive sequences and genome rearrangements.

Computational complexity in large genomes.

2. Synteny and Collinearity Analysis
Synteny refers to conserved blocks of gene order across species. Tools like MCScanX, SynMap, or CHITRA (for visualizing synteny interactively) detect these blocks to understand chromosomal evolution.

Use Case:
Studying ancient genome duplications in plants.

Investigating chromosomal rearrangements in cancer genomes.

3. Ortholog and Paralog Detection
Orthologs are genes in different species that evolved from a common ancestor, while paralogs are genes duplicated within a genome. Identifying them is crucial for functional annotation and evolutionary studies.

Popular Tools:
OrthoFinder, Orthologous MAtrix (OMA), InParanoid, and EggNOG.

Use Case:
Functional prediction of uncharacterized genes based on orthologs in model organisms.

Tracing gene family evolution.

4. Phylogenomic Analysis
Phylogenomic methods combine phylogenetics and genomics to infer evolutionary trees based on genome-wide data. These methods can handle dozens to hundreds of genomes, using concatenated alignments or gene trees.

Tools:
RAxML, IQ-TREE, ASTRAL, Phylip, BEAST.

Use Case:
Resolving the evolutionary relationships between microbial species.

Studying speciation events.

5. Pan-Genome Analysis
The pan-genome consists of the core genome (shared by all strains) and the accessory genome (strain-specific genes). This is especially popular in microbial genomics.

Tools:
Roary, Panaroo, BPGA, PGAP.

Use Case:
Understanding virulence factor diversity in E. coli.

Designing broad-spectrum vaccines.

6. Comparative Transcriptomics
Comparing transcriptomes across species or conditions reveals conserved and unique expression patterns. RNA-seq data can be mapped to reference genomes to identify orthologous expression profiles.

Use Case:
Comparing stress response in extremophiles and model species.

Studying conserved regulatory networks.

7. Functional Element Comparison
Beyond genes, comparative genomics also targets non-coding regions—enhancers, promoters, miRNAs. Conservation across species often implies functional importance.

Tools:
PhastCons, GERP, phyloP (based on multiple alignments).

Use Case:
Detecting conserved non-coding elements in vertebrates.

Studying regulatory divergence in human evolution.

8. Horizontal Gene Transfer (HGT) Detection
In microbes, genes often jump across species boundaries. Comparative genomics can detect HGT by identifying genes that defy the expected phylogenetic pattern.

Tools:
HGTector, DarkHorse, AlienHunter, SIGI-HMM.

Use Case:
Tracing antibiotic resistance genes.

Exploring microbial adaptability in extreme environments.

Final Thoughts
Comparative genomics is a powerful lens to observe the diversity and unity of life. With a broad toolkit—from aligners to orthology pipelines, phylogenetic engines to visualization tools—it allows scientists to ask big questions: How did genomes evolve? What makes species unique? Where do new genes come from?

Whether you're studying extremophiles, building better crops, or exploring human ancestry, comparative genomics offers the methods to connect the dots across the tree of life.

ADVERTISEMENT NO. - URDIP/ 5/2014

Learning opportunity for young Science and Engineering professionals to make a career in Information Science Industry CSIR has set up a Unit for Research and Development of Information Products (CSIR-URDIP) at Pune to work in the area of Scientific Informatics (ChemBioinformatics/Patent Informatics/Phytoinformatics/Toxinformatics) and related
software development projects.

Applications are invited from CSIR - UGC NET Qualified Candidates for consideration as Project Fellow (PF) and/or Senior Project Fellow (SPF) based on the experience to work on existing and new projects at CSIRURDIP.

Project Fellow

Remuneration - (Rs. 16,000.00 + 20% HRA)

M. Sc. In Biochemistry/Microbiology/Bioinformatics [Post-code A02] only with minimum of 55% marks

Senior Project Fellow

Remuneration - (Rs. 18,000.00 + 20% HRA)

M. Sc. in Biochemistry/Microbiology/Bioinformatics [Post-code A05] only with minimum of 55% marks plus two years research or relevant informatics experience

Please visit www.urdip.res.in/career.htm to apply online by 30th September, 2014.

Successful candidates who have appeared for NET exam in 2012 and 2013 are only eligible to apply.

Advertisement: http://115.112.95.114/urhr/download/Advt5_2014.pdf

The objective of this conference is two-fold:

Understanding different algorithms of MD and their relevant applications.
Hands-on practical exercises using NAMD.

More at http://ccbb.jnu.ac.in/advmdbio/

Stipend / Fellowship (consolidated)
Post-doctoral = Rs 50,000 per month
Post Masters = Rs 30,000 per month.

Duration of Fellowships:
Both Post-Doctoral and Post-Masters fellowships are for two years extendable to one more year depending on the progress of the project and decision of the technical committee.

The University Innovation Clusters established at the five Universities have their broad scientific areas under which BIRAC Innovation Fellows will be selected. The qualification and eligibility of each UIC has been mentioned below.

Who can apply?
BIRAC along with five UICs invites research proposals from:

 Applicants who have completed their Master/ Ph.D. on and after 1st January 2014 for
Post Masters and Post-Doctoral BIRAC Innovation Fellowships

Applicants will have to submit an online application in the prescribed format. Each application will be reviewed by an expert committee at each UIC, which applicant has chosen. Applications will be identified on the identified criteria. Selected applicants will be called for a detailed project presentation and personal interview in front of an expert committee for final selection of the BIRAC Innovation Fellows.

Mere fulfilling the eligibility criterion does not entitle applicants to be called for interview.

More at http://birac.nic.in/webcontent/UIC_Fellowships_Qualification_Eligibility.pdf

More http://www.nieduszynski.org/index.php
http://www.path.ox.ac.uk/research/cell-biology-and-pathology/conrad-nieduszynski-group

The Academy has an International Exchange Programme with Academies/Organizations in the countries: Brazil, China, France, Hungary, Iran, Israel, Nepal, Philippines, Poland, Scotland, Slovak Republic, Republic of Slovenia, Sudan and Taiwan.

Applications are invited from Indian Nationals for consideration by the Academy for the next calendar year.

• The applicant should be a scientist holding a regular (permanent) position in a recognized S & T Institution/University and actively engaged in research work in frontline areas.
• He/She should not have been abroad during the last 3 years under any INSA Programme.
• The scientist should have been accepted to work in an Institute/Laboratory in the country to be visited and this should be supported by a letter of invitation from the host abroad.
• Those who wish to visit abroad for three months should submit a detailed programme of their collaborative research work to be conducted.

All applications duly completed should be forwarded to the academy through proper channel by the employer/head of the Institute.

• Scientists selected for deputation abroad would be provided 100% travel support (by only Air India excursion class airfare, through shortest route from the place of duty in India to the nearest airport of host Institute and back) by INSA.
• Medical Insurance purchased in India.
• Visa fee (if any).
• The receiving Academy/Organization would provide local hospitality including internal travel abroad.

Contact for detail at 

www.insaindia.res.in

INDIAN NATIONAL SCIENCE ACADEMY
Bahadur Shah Zafar Marg, New Delhi – 110 002.
Telephone: 91-11-23221931 – 23221950 (EPABX),
Fax: 91-11- 23235648, 23231095