No of post : 01
Essential qualifications: i) Ph. D degree in Bioinformatics/computers/Bio-technology. OR ii) Master’s Degree in Bioinformatics/computers/Bio-technology with 1st division or 60% marks or equivalent overall grade point average with at least two years of research experience as evidenced from fellowship/Associateship/training/other engagements.
Desirable qualifications: i) Working Knowledge and Published Research papers in Bio-informatics.
Monthly emoluments : Rs. 23,000/- + HRA . for M.Sc degree holder Rs. 24,000/- + HRA for Ph.D degree holder
Maximum Age limit : Research Associate – Males- 40 years & Women 45 years.
SELECTION PROCEDURE FOR CENTRAL POTATO RESEARCH INSTITUTE (CPRI) – RESEARCH ASSOCIATE POST:

Written Test on 20/03/2015.
Shortlisted candidates will undertake face to face interview.
Dates are yet to be announced for the final selection
WALK-IN PROCEDURE FOR RESEARCH ASSOCIATE VACANCY IN CENTRAL POTATO RESEARCH INSTITUTE (CPRI):

Interested/eligible candidates should submit their application along with the attested copies of educational qualification (provisional degree of Masters and Ph.D is mandatory )/experience certificates and one passport size photograph to the Asstt. Admn. Officer(E-I), CPRI, Shimla-171001 at 9.30 AM on the date of interview. The candidates appearing for interview must bring original certificate with them and only those candidates possessing essential qualification as per advertisement will be interviewed. The Director, CPRI, Shimla reserves the right either to fill up the post or cancel the interview without assigning any reasons thereof. Application form is available in the website ( website: http//cpri.ernet.in). No TA/DA will be given by the Institute to the candidates. The Institute is located at Bemloe which is about 2 Kms from Main Bus Stand(Old)/3 Kms. from the Railway Station and about 5 Kms. from ISBT (Tutikandi).

https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2017/Day1/Session4-seqIntro.html

Address of the bookmark: https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2017/Day1/Session4-seqIntro.html

PRINCIPAL SCIENTIST Pay Band: Minimum pay of `43,000 in the PB-4 of `37400-67000/- + RGP of `10,000/-.

Age: The candidates must not have attained the age of 52 years as on 24.03.2015. There shall be no age limit for the Council’s employees.

ICAR-NATIONAL INSTITUTE OF BIOTIC STRESS MANAGEMENT, RAIPUR (CHHATTISGARH)

57. Principal Scientist (Agricultural Entomology) (Two post)

Qualifications Essential:

(i) Doctoral degree in Agricultural Entomology including relevant basic sciences.

(ii) 10 years experience in the relevant subject out of which at least 8 years should be as Scientist/ Lecturer/Extension Specialist or in an equivalent position in the Pay Band- 3 of `15600-39100 with Grade Pay of `5400/`6000/`7000/`8000 and 2 years as a Senior Scientist or in an equivalent position in the Pay Band- 4 of ` 37400-67000 with Grade Pay of ` 8700/ ` 9000.

(iii) The candidate should have made contribution to research/teaching/extension education as evidenced by published work/innovations and impact.

Desirable:

(i) Experience of using frontiers research tools in management of insect pests of crop plants.

(ii) Evidence of contributions to relevant field through publications/ patents/citation index to suggest a vision/perspective in biotic stress research.

61. Principal Scientist (Bioinformatics) (One post)

Qualifications Essential:

(i) Doctoral degree in Bioinformatics including relevant basic sciences. (ii) & (iii) As in item no. 57 above.

Desirable:

(i) Experience of using bioinformatics for advancement of knowledge and for research on biotic stress management.

(ii) Evidence of contributions to relevant field through publications/patents/citation index to suggest a vision/perspective in biotic stress research.

http://asrb.org.in/administrator/uploads_dir/1424859407english.pdf

Study of 10 tools on five datasets that such a comparative evaluation of these tools is hindered by two types of circularity: they arise due to (1) the same variants or (2) different variants from the same protein occurring both in the datasets used for training and for evaluation of these tools, which may lead to overly optimistic results. Comparative evaluations of predictors that do not address these types of circularity may erroneously conclude that circularity confounded tools are most accurate among all tools, and may even outperform optimized combinations of tools.

Following tools are useful for mis sense muation detection ... 

PolyPhen‐2 (PP2)
“Predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations”

MutationTaster‐2 (MT2)
“Evaluation of the disease‐causing potential of DNA sequence alterations”

MutationAssessor (MASS)
“Predicts the functional impact of amino acid substitutions in proteins, such as mutations discovered in cancer or missense polymorphisms”

LRT
“Identify a subset of deleterious mutations that disrupt highly conserved amino acids within protein‐coding sequences, which are likely to be unconditionally deleterious”

SIFT
“Predicts whether an amino acid substitution affects protein function”

GERP++
“Identifies constrained elements in multiple alignments by quantifying substitution deficits. These deficits represent substitutions that would have occurred if the element were neutral DNA, but did not occur because the element has been under functional constraint. We refer to these deficits as “rejected substitutions.” Rejected substitutions are a natural measure of constraint that reflects the strength of past purifying selection on the element”

phyloP
“Compute conservation or acceleration P values based on an alignment and a model of neutral evolution”

FatHMM unweighted (FatHMM‐U)
Predicts “functional consequences of both coding variants, that is, nonsynonymous single‐nucleotide variants, and noncoding variants”

FatHMM weighted (FatHMM‐W)
Predicts “functional consequences of both coding variants, that is, nonsynonymous single‐nucleotide variants, and noncoding variants” and its weighting scheme attributes higher tolerance scores to SNVs in proteins, related proteins, or domains that already include a high fraction of pathogenic variantsh

Combined Annotation Dependent Depletion (CADD)
“CADD is a tool for scoring the deleteriousness of single‐nucleotide variants as well as insertion/deletions variants in the human genome”

ICAR-NPTC: Fibre development in flax/linseed.

(Job # 1) Research Associate (one) (Bioinformatics)

Rs.24000+ 30% HRA) for Ph.D. and for M. Sc Rs.23000/‐ (+ 30% HRA)

Ph.D. Degree in Bioinformatics/Molecular Biology/Biotechnology/ Genetics/allied sciences; or M. Sc in Bioinformatics/ Biotechnology/Life Sciences/ allied sciences with 1st division or 60% marks or equivalent overall grade point average with at least two years of research experience as evidenced from Fellowship/ Associate ship. 2 years research experience in bioinformatic data analysis/molecular biology techniques, and high throughput DNA/RNA sequencing, and transcriptome data analysis. Research paper with IF>1 will be desirable

ICAR-NPTC: Shade avoidance/low-light tolerance in rice.

General Terms & Conditions applicable to all the positions:
Age Limit: 35 years max. (5 years relaxation for SC/ST/OBC and woman candidates as per ICAR rules).
The positions are purely temporary, on a contractual basis and are initially offered for one year.
Originals must be shown for verification. 7. Research experience (Experience certificate from previous employer to be attached): I hereby declare that the information provided above is true to the best of my knowledge. Date: Signature

Advertisement:

www.nrcpb.org/sites/default/files/ICAR-NPTC%20DBT%20RA%20SRF%20interview%2024th%20March.pdf

##################################################
[Mon May 7 11:29:18 2018] Reduction...
#file name genome size contigs heterozygous size [%] heterozygous contigs [%] identity [%] possible joins homozygous size [%] homozygous contigs [%]
/usr/lib/python2.7/dist-packages/matplotlib/font_manager.py:273: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment.
warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.')
test/run1/contigs.fa 163897 245 66377 40.50 221 90.20 94.854 0 97520 59.50 24 9.80

##################################################
[Mon May 7 11:29:29 2018] Estimating parameters of libraries...
Aligning 19504 mates per library...
Insert size statistics Mates orientation stats
FastQ files read length median mean stdev FF FR RF RR
test/5000_1.fq.gz test/5000_2.fq.gz 50 4998 4990.20 721.47 0 4674 0 0
test/600_1.fq.gz test/600_2.fq.gz 100 599 598.63 47.68 0 10000 0 0

##################################################
[Mon May 7 11:29:29 2018] Scaffolding...
iteration 1.1: test/run1/contigs.reduced.fa 24 97520 39.355 17 94157 7321 2195 0 29603
19505 pairs. 17302 passed filtering [88.71%]. 1627 in different contigs [8.34%].
1526 pairs. 558 in different contigs [36.57%].
iteration 1.2: test/run1/_sspace.1.1.fa 3 97626 39.344 3 97626 87536 6063 821 87536
19505 pairs. 17607 passed filtering [90.27%]. 182 in different contigs [0.93%].
1077 pairs. 124 in different contigs [11.51%].
iteration 2.1: test/run1/_sspace.1.2.fa 3 97626 39.344 3 97626 87536 6063 821 87536
19505 pairs. 15112 passed filtering [77.48%]. 1295 in different contigs [6.64%].
3417 pairs. 396 in different contigs [11.59%].
iteration 2.2: test/run1/_sspace.2.1.fa 1 99133 39.344 1 99133 99133 99133 2328 99133
19505 pairs. 15152 passed filtering [77.68%]. 0 in different contigs [0.00%].
3398 pairs. 0 in different contigs [0.00%].

##################################################
[Mon May 7 11:29:34 2018] Gap closing...
iteration 1.1: test/run1/scaffolds.fa 1 99133 39.344 1 99133 99133 99133 2328 99133

##################################################
[Mon May 7 11:29:35 2018] Final reduction...
#file name genome size contigs heterozygous size [%] heterozygous contigs [%] identity [%] possible joins homozygous size [%] homozygous contigs [%]
[WARNING] Nothing reduced!
test/run1/scaffolds.filled.fa 99390 1 0 0.00 0 0.00 0.000 0 99390 100.00 1 100.00

##################################################
[Mon May 7 11:29:35 2018] Reporting statistics...
#fname contigs bases GC [%] contigs >1kb bases in contigs >1kb N50 N90 Ns longest
test/contigs.fa 245 163897 40.298 24 117391 3975 233 0 29603
test/run1/contigs.fa 245 163897 40.298 24 117391 3975 233 0 29603
test/run1/contigs.reduced.fa 24 97520 39.355 17 94157 7321 2195 0 29603
test/run1/_sspace.1.1.fa 3 97626 39.344 3 97626 87536 6063 821 87536
test/run1/_sspace.1.2.fa 3 97626 39.344 3 97626 87536 6063 821 87536
test/run1/_sspace.2.1.fa 1 99133 39.344 1 99133 99133 99133 2328 99133
test/run1/_sspace.2.2.fa 1 99133 39.344 1 99133 99133 99133 2328 99133
test/run1/scaffolds.fa 1 99133 39.344 1 99133 99133 99133 2328 99133
test/run1/_gapcloser.1.1.fa 1 99390 39.689 1 99390 99390 99390 2 99390
test/run1/scaffolds.filled.fa 1 99390 39.689 1 99390 99390 99390 2 99390
test/run1/scaffolds.reduced.fa 1 99390 39.689 1 99390 99390 99390 2 99390

##################################################
[Mon May 7 11:29:35 2018] Cleaning-up...
#Time elapsed: 0:00:17.376924

A postdoctoral training position is currently available in the Computational and Statistical Genomics Branch (CSGB) of the National Human Genome Research Institute (NHGRI). The position is located in the laboratory of Andy Baxevanis, Ph.D., whose research group uses comparative genomics approaches to better-understand the molecular innovations that drove the surge of diversity in early animal evolution. The overarching theme of Dr. Baxevanis’ research program is focused on how non-traditional animal models convey critical insights into human disease research.

Candidates should have or be close to obtaining a Ph.D. or equivalent degree in bioinformatics, computational biology, computer science, molecular biology, or a closely related field. Candidates with a background in evolutionary biology are particularly encouraged to apply. Programming skills and experience in the application of computational methods to genomic data are highly desirable. Applicants must possess good communication skills and be fluent in both spoken and written English. The ability to learn how to use new software and quickly become expert in its use, critical thinking, problem-solving abilities, and the ability to work semi-independently are required.
How to Apply

Interested applicants should submit a curriculum vitae, a detailed letter of interest, and the names of three potential referees to Dr. Baxevanis at andy@mail.nih.gov.
About Our Organization

The NIH Intramural Research Program is on the Bethesda, Maryland campus and offers a wide array of training opportunities for scientists early in their careers. The funding for this position is stable and offers the trainee wide latitude in the design and pursuit of their research project. The successful candidate will have access to NHGRI’s established and robust bioinformatics infrastructure, as well as resources made available through NIH’s Center for Information Technology (CIT) and the National Center for Biotechnology Information (NCBI).

For more information on CSGB and NHGRI’s Intramural Research Program, please see http://genome.gov/DIR/.

The mmgenome R package also facilitates effortless integration with additional data sources and hence should not be seen as "yet another binning method", but rather a package to integrate different binning strategies.

All functions in the mmgenome R package has associated documentation, check it out in R by e.g. ?mmplot.

Address of the bookmark: https://github.com/MadsAlbertsen/mmgenome

ESSENTIAL QUALIFICATION: PH.D. DEGREE IN LIFE SCIENCES / PHYSICAL SCIENCE.

Research Associate for Programme No. –I Specialization in the area of plant molecular biology or plant proteomic study or plant pathogen interaction.
Research Associate for Programme No. –I Specialization in the area of plant / fungal Biotechnology, tissue culture and molecular biology
Research Associate for Programme No. –III Specialization in the area of structural biology and protein crystallography.
Research Associate for Programme No. – V Specialization in the area of microbial physiology (metabolism) or environmental microbiology, with experience in microbial genomics and proteomics.
Research Associate for Programme No. – VII Specialization in the area of Theoretical High Energy Astrophysics or Astroparticle Physics. Proven record of independent research experience in Astrophysical
Radiation Magnetohydrodynamics or Cosmic Ray Astrophysics. Experience in numerical techniques and /or date analysis would be additional advantage.
Associateship : 22,000/- p.m., plus admissible H.R.A. and Medical benefit.
Age: Below 3 Age : Below 35 years (Relaxable in case of SC/ST/OBC/Women candidates only as per rule).
SELECTION PROCEDURE FOR BOSE INSTITUTE- RESEARCH ASSOCIATE POST:

Candidates can apply on or before 13/4/2015.
No detailed information about the selection procedure is mentioned in the recruitment notification.
HOW TO APPLY FOR RESEARCH ASSOCIATE VACANCY IN BOSE INSTITUTE:

Interested and eligible candidates may read the application procedures and instructions carefully before applying through online as well as submitting the hard copy of the same. Candidates those who has submitted their Ph.D. Thesis and can produce Provisional Ph.D. Certificate at the time of Interview may also apply

Ref
Bose Institute Recruitment 2015 – ADVT. NO. : BI/IF/35/2014-15.

1. MISA: MISA (MIcroSAtellite) is a web-based tool that can identify SSRs in DNA sequences. It can be used to analyze nucleotide sequences from various organisms and can identify perfect, compound, and imperfect SSRs.

2. SSR Locator: SSR Locator is a web-based tool that identifies SSRs in both DNA and RNA sequences. It can identify perfect, compound, and imperfect SSRs, and can also filter out low complexity regions.

3. SciRoKo: SciRoKo is a software tool that can identify SSRs in DNA sequences. It can be used to analyze genomic and transcriptomic sequences from various organisms and can identify perfect, compound, and imperfect SSRs.

4. Primer3: Primer3 is a web-based tool that designs PCR primers for SSRs. It can design primers for perfect and imperfect SSRs, and can be used to design primers for SSRs in various organisms.

5. QDD: QDD (Quick Detection of Duplication) is a software tool that can identify SSRs in DNA sequences and can also identify duplicate loci. It can be used to analyze genomic and transcriptomic sequences from various organisms.

These are just a few examples of the many bioinformatics tools available for exploring SSRs. Depending on your specific needs and research questions, you may find that other tools are more appropriate for your analysis.