What are SNPs?
SNPs (pronounced "snips") are positions in the genome where individuals differ by a single nucleotide. For example:

Reference: ...A T G C A T G A...
Variant:     ...A T G T A T G A...

Here, the C in the reference genome has been replaced by a T in the variant.

SNPs occur roughly every 300–1,000 bases in the human genome, meaning there are millions of them scattered throughout our DNA. Most SNPs have no effect on health, but some are linked to disease susceptibility, drug response, and other traits.

Why Do We Analyze SNPs?
1. Medical Genetics

Identify disease-associated variants (e.g., BRCA1/2 in breast cancer).

Predict drug response (pharmacogenomics).

Enable precision medicine by tailoring treatments.

2. Population Genetics & Ancestry

Trace human migration and ancestry.

Study genetic diversity within and between populations.

3. Agriculture & Animal Breeding

Select for desirable traits (drought resistance, yield, disease resistance).

Improve breeding efficiency in livestock.

4. Evolutionary Biology

Track natural selection.

Study adaptation in wild populations.

How is SNP Analysis Performed?
SNP analysis can be broadly divided into three steps:

SNP Detection
Genotyping arrays: Chips that test hundreds of thousands of known SNP positions simultaneously. Fast and affordable, widely used in consumer ancestry testing.

Whole-genome or whole-exome sequencing: Can detect known and novel SNPs across the genome.

Targeted sequencing or PCR: For focused analysis of specific regions.

Variant Calling
Sequencing data is aligned to a reference genome. Bioinformatics tools (e.g., GATK, bcftools) identify positions where the sequenced sample differs from the reference.

Annotation and Interpretation
Tools (e.g., SnpEff, VEP) predict the functional impact of SNPs.

Are the SNPs in coding regions? Do they cause amino acid changes? Are they known to be pathogenic?

Databases like dbSNP, ClinVar, and GWAS Catalog provide information on known associations.

Common Tools for SNP Analysis
Alignment: BWA, Bowtie2

Variant Calling: GATK, FreeBayes

Visualization: IGV, UCSC Genome Browser

Annotation: SnpEff, VEP

Statistical Analysis: PLINK, SNPTEST

Challenges in SNP Analysis
False positives/negatives: Sequencing errors, alignment issues.

Population stratification: Confounding in association studies.

Interpretation: Many SNPs have unknown or complex effects.

Researchers address these with rigorous quality control, large datasets, and increasingly sophisticated statistical models.

The Future of SNP Analysis
With advances in sequencing technology and AI-driven analysis, SNP studies are expanding:

Polygenic risk scores predict disease risk based on thousands of SNPs.

Large-scale biobanks (e.g., UK Biobank, All of Us) enable powerful genome-wide association studies (GWAS).

CRISPR and functional assays help validate SNP effects in the lab.

SNP analysis is at the heart of the genomic revolution, promising insights into biology, health, and evolution at unprecedented scale.

Conclusion
From diagnosing rare diseases to designing better crops, SNP analysis is a foundational tool in modern science. As our ability to sequence and interpret genomes improves, so will our understanding of these tiny—but mighty—variations in DNA.

ICAR-INDIAN AGRICULTURAL RESEARCH INSTITUTE

L.B.S Building, Pusa Campus,

New Delhi-110012

Walk-in-Interview: 18th December 2015

DBT funded project: Distributed Information Centre under BTISnet (PI: Dr. A.K.Mishra)

Senior Research Fellow Two

Rs 28000/- + HRA

i) Master’s degree in Bioinformatics or Computer Science+ NET qualification and two years research experience, or

ii) M. Tech degree in Bioinformatics or Computer Science /Engineering with two years research experience Efficiency to handle agricultural databases and bioinformatics tool development

#Junior Research Fellow

Rs. 25000/- + HRA

i) Master’s degree in Bioinformatics or Computer Science + NET qualification, or

ii) M. Tech degree in Bioinformatics or Computer Science/Engineering Efficiency to handle agricultural databases and bioinformatics tool development

Traineeship Two

Rs. 8000/- consolidated

M.Sc./M. Tech (Bioinformatics) with 60 % marks from a recognized University

Studentship Four

Rs. 8000/- consolidated

Final year M.Sc./ M.Tech (Bioinformatics) Students from a recognized University

* M. Tech with Four Years Bachelor’s degree followed by Master’s degree

# In case suitable person is not found for SRF position, it may be filled at the JRF level The interview will be held on 18 th December 2015 at 10:00 AM at AKMU, LBS Building, IARI, Pusa Campus, New Delhi-110012. Terms and Conditions:  Maximum age limit is 35 years for all positions. Age relaxation of 5 yrs for SC/ST/OBC and woman candidates will be given.  The above post is purely temporary and is co-terminus with the project. The candidate shall not claim for regular appointment.  No TA/DA will be paid for attending the interview.  Bring self attested copies and originals of all certificates ( class 10th )onwards along with biodata in the attached format, proof of date of birth, one passport size photo, NOC from present employer, if any  Canvassing in any form will disqualify the candidate. 

Reporting time for interview: 9.30-10.00 AM at AKMU, IARI, New Delhi -110 012

Advertisement:

www.iari.res.in/files/SRF_JRF_Akkmu-27112015-20151127-124003.pdf

1. FASTA
2. FASTQ
3. SAM
4. BAM
5. VCF
6. GFF
7. GTF

Address of the bookmark: https://bioinformatics.uconn.edu/resources-and-events/tutorials/file-formats-tutorial/

Research Associate (one post): Emoluments as per DST/DBT norms & as sanctioned in the project
Qualification: Candidates having Ph.D. degree (awarded) in Life Sciences/Molecular Biology/Bioinformatics or related field are eligible to apply.

Junior Research Fellow (one post): Emoluments as per DST/DBT norms & as sanctioned in the project
Qualification: Candidates having M.Sc. degree or equivalent (with minimum 55% marks) in Life Sciences, Biotechnolgy, Bioinformatics, Molecular Biology or any other related field are eligible to apply

Additional Information

Address:
Staff Scientist
National Institute of Plant Genome Research (NIPGR)
Aruna Asaf Ali Marg, P.O. Box NO. 10531,
New Delhi - 110067

States & U.T
State & Union Territories Delhi

How To Apply

Apply Details
Eligible candidates may apply by sending their complete application in the given format. The attested copies of the certificates and proof of research experience (if any) are to be attached with the hard copy of application. The applications should reach at the address given below within 15 days from the date of advertisement.

Web/Notification URL
http://www.nipgr.res.in/careers/vacancie s_latest.php

Eligibility : ME/M.Tech(Bio-Informatics/Bio-Chemistry Engg), MSc(Bio-Informatics), BE/B.Tech

Location : Pune

Last Date : 16 Nov 2015

Hiring Process : Face to Face Interview

No. Bio/NCIM/3

Project Assistant II Jobs opportunity in National Chemical Laboratory (NCL) on temporary basis

Project Code No. : GAP312626

Title of the Project : Microbial ecology and distribution of geochemical cycling genes in an hot spring ecosystem

No. of Post : 01

Qualifications : M.Sc./B.Tech/M.Tech in Computational biology/ Bioinformatics from recognized university with minimum 60 % marks (aggregate)

Desirable : Good knowledge of computational skills, Linux (command line and GUI) and Unix; Perl / Python / R /C-programming. Practical knowledge of analysis of Next generation sequence datasets (amplicon sequencing, whole metagenome, and complete genome sequencing) with reference to microbes. Analysis and statistical validation of NGS data generated from different chemistry platforms. Some wet-lab experience in microbial system would be an added advantage as project involves some travel.

Emoluments : Rs. 16,000/-

Age Limit : 28 years

The application with the above information duly signed together with photo-copies of relevant certificates/testimonials should be addressed to : The Head, NCIM Resource Centre (Attn Dr. M.S. DHARNE), National Chemical Laboratory, Pune 411 008, so as to reach on or before 16th November 2015.

More at http://www.ncl-india.org/files/JoinUs/JobVacancies/TemporaryJobs.aspx?menuid=ql6&childmenustripid=divSubQL6

The BioComputing UP Laboratory, headed by Prof. Silvio Tosatto, is a dynamic group of a dozen people working on several aspects of prediction of protein structure & function employing techniques at the intersection between biology, medicine, chemistry, physics & computer science.
Our aim is to integrate the development of novel methods and their application to biologically relevant problems.

We are looking for candidates with a solid Bioinformatics background, programming experience (Python, C++ and/or Java) and good knowledge of molecular biology (protein structure/function). Good knowledge of statistics as well as experience in using database systems (MongoDB, MySQL and/or Postgres) is desirable. Candidates should have a degree with top marks, optionally hold a PhD, and be highly motivated to work on interdisciplinary research. Good knowledge of English, an open-minded spirit, being collaborative and creative are crucial.

The fellowship, which should start as soon as possible, is renewable and initially for one year. It will be commensurate to experience, can be extended depending on performance and may lead to a PhD degree. The successful candidate will be working full-time at the BioComputing UP Laboratory, University of Padova. Travel support for conferences and/or research visits abroad is provided.
To apply, please send your CV, with a motivation letter and brief description of your research background as well as the names of two (or more) references to: biocomp@bio.unipd.it.

Start date: As soon as possible

Duration: 1 year, renewable

Salary on grant: Commesurate to experience

Contact Person (Referent): Silvio Tosatto

Ref. E-Mail: biocomp@bio.unipd.it

Tel: +39 049 827 6269
Fax: +39 049 827 6260

Group Web Page: http://protein.bio.unipd.it/

LAST can:

• Handle big sequence data, e.g:
  • Compare two vertebrate genomes
  • Align billions of DNA reads to a genome
• Indicate the reliability of each aligned column.
• Use sequence quality data properly.
• Compare DNA to proteins, with frameshifts.
• Compare PSSMs to sequences
• Calculate the likelihood of chance similarities between random sequences.
• Do split and spliced alignment.
• Train alignment parameters for unusual kinds of sequence (e.g. nanopore).

Address of the bookmark: http://last.cbrc.jp/

PGIMER

Chandigarh

invites application for a project dissertation program for students who have completed their first year of M.Sc. in Bioinformatics.

This is an exciting opportunity for Master's students to train in modern methods in Bioinformatics. The duration of the training will be four to six months, starting from January 2016.

Education: Pursuing M.Sc. Bioinformatics

Essential: Post graduate applicants should have completed their first year and should be in the third semester or first half of the second year.

Only students who are willing to spend a minimum period of 4 months to a maximum of six months, without any break, would be eligible for the program.

How to Apply: Candidates interested in the above project dissertation program should apply online. Send your CV, Scanned copy of letter of recommendation from Head of Institution along with Registration form in the given format should be sent to: info@bicpgi.org

Please mention clearly “Project dissertation & your Name” in the Subject.

The last date for application is December 23, 2015

Note: Selected candidates may please note that the program is free of cost and would not provide any financial aid for transport and stay. Name of the selected candidates would be posted on the centre website by December 31, 2015.

Incomplete applications will be rejected.

For more information visit our website: http://bic-pgi.org/

Jamia Hamdard New Delhi - 110062 Additional Information States & U.T State & Union Territories Delhi How To Apply Apply Details
Last date of application: December 5, 2015 Web/Notification URL http://www.jamiahamdard.ac.in/

Applications are invited in the prescribed form for filling up the following posts of Teachers and Service Personnel from the candidates who are qualified as on the last date fixed for receipt of applications in the University of Agricultural Sciences, Dharwad.

I. ASSISTANT PROFESSOR CADRE (Scale of pay Rs.15600-39100 + AGP Rs. 6000) (UGC / ICAR pay-scales)

I. Re-notified posts:

9. Assistant Professor of Bioinformatics 1 GM-1

More Info : https://sites.google.com/a/uasd.in/recruitment/