Department of Biotechnology, Government of India, New Delhi & Pondicherry University, Puducherry

Starting of online submission of application : April 13, 2016

Last date for submission of application : May 13, 2016

Examination consists of two parts:

Part - I (Paper - I) : June 12, 2016 (10 AM -12 PM)
Part - II (Paper • II & III) : June 26, 2016 (9 AM • 12 PM & 2 PM • 4 PM)

Objective: Pondicherry University, on behalf of the Department of Biotechnology (DBT),
Government of India, will conduct the Bioinformatics National Certification (BING) examination. The objective of this examination is to identify Bioinformatics professionals
for further studies as well as to help potential employers in recruitment of candidates having exceptionally good Bioinformatics skills.

Eligibility : Bachelor degree in Life Sciences, Physical Sciences, Chemical Sciences, Mathematical Sciences, Agriculture, Veterinary, Medicine, Pharmacy, Engineering and Technology are eligible to appear for the examination. They need not have any formal training, diploma or certificate in Bioinformatics.

Application and syllabus : The online application can be filled from April 13, 2016 to May 13, 2016.

Syllabus for the examination is available online.

It consists of five sections:
Bioinformatics, Biology, Physical and Chemical Sciences, Mathematics & Statistics and Computer Science & Information Technology.

Examination : The examination fee is Rs. 600/- for general candidates, Rs. 400/- for women/OBC candidates and Rs. 200 for SC/ST candidates, and no fee for physically challenged candidates.

The online Part - I (Paper - I) examination is scheduled on June 12,2016 and Part- II (Paper - II and Paper- III) on June 26, 2016. The Paper- I will be of objective type and candidates scoring a minimum of 40% marks in Paper - I will be called to appear in Part II examination.

Part II examination consists of two papers : The Paper - II will be of short answer type questions of three hours duration while the Paper- III will be a practical examination of two hours duration to test analytical ability and programming skill of candidates.

Research Fellowships for all the successful candidates those who are interested and qualified in pursuing Ph.D. in India will be awarded. In addition, cash prizes will be awarded to the top 10 successful candidates.

The details of examination centres, other details and submission of application, please
visit: http://www.pondiuni.edu.in/exams/binc/

Department of Biotechnology, Government of India, New Delhi & Pondicherry University, Puducherry

Starting of online submission of application : April 13, 2016

Last date for submission of application : May 13, 2016

Examination consists of two parts:

Part - I (Paper - I) : June 12, 2016 (10 AM -12 PM)
Part - II (Paper • II & III) : June 26, 2016 (9 AM • 12 PM & 2 PM • 4 PM)

Objective: Pondicherry University, on behalf of the Department of Biotechnology (DBT),
Government of India, will conduct the Bioinformatics National Certification (BING) examination. The objective of this examination is to identify Bioinformatics professionals
for further studies as well as to help potential employers in recruitment of candidates having exceptionally good Bioinformatics skills.

Eligibility : Bachelor degree in Life Sciences, Physical Sciences, Chemical Sciences, Mathematical Sciences, Agriculture, Veterinary, Medicine, Pharmacy, Engineering and Technology are eligible to appear for the examination. They need not have any formal training, diploma or certificate in Bioinformatics.

Application and syllabus : The online application can be filled from April 13, 2016 to May 13, 2016.

Syllabus for the examination is available online.

It consists of five sections:
Bioinformatics, Biology, Physical and Chemical Sciences, Mathematics & Statistics and Computer Science & Information Technology.

Examination : The examination fee is Rs. 600/- for general candidates, Rs. 400/- for women/OBC candidates and Rs. 200 for SC/ST candidates, and no fee for physically challenged candidates.

The online Part - I (Paper - I) examination is scheduled on June 12,2016 and Part- II (Paper - II and Paper- III) on June 26, 2016. The Paper- I will be of objective type and candidates scoring a minimum of 40% marks in Paper - I will be called to appear in Part II examination.

Part II examination consists of two papers : The Paper - II will be of short answer type questions of three hours duration while the Paper- III will be a practical examination of two hours duration to test analytical ability and programming skill of candidates.

Research Fellowships for all the successful candidates those who are interested and qualified in pursuing Ph.D. in India will be awarded. In addition, cash prizes will be awarded to the top 10 successful candidates.

The details of examination centres, other details and submission of application, please
visit: http://www.pondiuni.edu.in/exams/binc/

The latest version is 1.2.4.

To cite Platanus, please use the following:

Kajitani R, Toshimoto K, Noguchi H, Toyoda A, Ogura Y, Okuno M, Yabana M, Harada M, Nagayasu E, Maruyama H, Kohara Y, Fujiyama A, Hayashi T, Itoh T, “Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads”. Genome Res. 2014 Aug;24(8):1384-95. doi: 10.1101/gr.170720.113. [abstract | full text]

Address of the bookmark: http://platanus.bio.titech.ac.jp/

Address of the bookmark: http://genetics.bwh.harvard.edu/pph2/

http://gkno.me/how-to/install.html

http://gkno.me/software.html

Address of the bookmark: http://gkno.me/

In the mid 1960's scientists discovered that many genomes contain stretches of highly repetitive DNA sequences ( see Reassociation Kinetics Experiments, and C-Value Paradox ). These sequences were later characterized and placed into five categories:

Simple Repeats - Duplications of simple sets of DNA bases (typically 1-5bp) such as A, CA, CGG etc.
Tandem Repeats - Typically found at the centromeres and telomeres of chromosomes these are duplications of more complex 100-200 base sequences.
Segmental Duplications - Large blocks of 10-300 kilobases which are that have been copied to another region of the genome.
Interspersed Repeats
Processed Pseudogenes, Retrotranscripts, SINES - Non-functional copies of RNA genes which have been reintegrated into the genome with the assitance of a reverse transcriptase.
DNA Transposons
Retrovirus Retrotransposons
Non-Retrovirus Retrotransposons ( LINES )

Currently up to 50% of the human genome is repetitive in nature and as improvements are made in detection methods this number is expected to increase.

On the other hand; In genetics, the term palindrome refers to a sequence of nucleotides along a DNA (deoxyribonucleic acid) or RNA (ribonucleic acid) strand that contains the same series of nitrogenous bases regardless from which direction the strand is analyzed. Akin to a language palindrome—wherein a word or phrase is spelled the same left-to-right as right-to-left (e.g., the word RADAR or the phrase "able was I ere I saw elba")—with genetic palindromes it does not matter whether the nucleic acid strand is read starting from the 3' (three prime) end or the 5' (five prime) end of the strand.

Recent research on palindromes centers on understanding palindrome formation during gene amplification. Other studies have attempted to relate palindrome formation to molecular mechanisms involved in double stranded breaks and in the formation of inverted repeats. Assisted by high speed computers, other groups of scientists link palindrome formation to the conservation of genetic information.

Related to the direction of transcription by RNA polymerase, DNA strands have upstream and downstream terminus defined by differing chemical groups at each end. The ends of each strand of DNA or RNA are termed the 5' (phosphate bound to the 5' position carbon) and 3' (phosphate bound to the 3' carbon) ends to indicate a polarity within the molecule. Using the letters A, T, C, G, to represent the nitrogenous bases adenine, thymine, cytosine, and guanine found in DNA, and the letters A, U, C, G to represent the nitrogenous bases adenine, uracil, cytosine, guanine found in RNA (Note that uracil in RNA replaces the thymine found in DNA), geneticists usually represent DNA by a series of base codes (e.g., 5' AATCGGATTGCA 3'). The base codes are usually arranged from the 5' end to the 3' end.

Because of specific base pairing in DNA (i.e., adenine (A) always bonds with (thymine (T) and cytosine (C) always bonds with guanine (G)) the complimentary stand to the sequence 5' AATCGGATTGCA 3' would be 3' TTAGCCTAACGT 5'.

With palindromes the sequences on the complimentary strands read the same in either direction. For example, a sequence of 5' GAATTC3' on one strand would be complimented by a 3' CTTAAG 5' strand. In either case, when either strand is read from the 5' prime end the sequence is GAATTC. Another example of a palindrome would be the sequence 5' CGAAGC 3' that, when reversed, still reads CGAAGC.

Palindromes are important sequences within nucleic acids. Often they are the site of binding for specific enzymes (e.g., restriction endobucleases) designed to cut the DNA strands at specific locations (i.e., at palindromes).

Palindromes may arise from brakeage and chromosomal inversions that form inverted repeats that compliment each other. When a palindrome results from an inversion, it is often referred to as an inverted repeat. For example, the sequence 5' CGAAGC 3', if inverted (reversed 180°), still reads CGAAGC.

The European Molecular Biology Open Software Suite (EMBOSS) includes some basic tools for finding tandem repeats and inverted repeats (see B.6.22. Applications in group Nucleic:repeats). There are many on-line services providing the EMBOSS tools, for example:

• Wageningen Bioinformatics Webportal EMBOSS explorer
• Mobyle@Pasteur
• Soaplab2 Web Services at Vital-IT

For more sophisticated repeat finding you will want to look at tools using Repbase for example:

• CENSOR
  • CENSOR@GIRI
  • CENSOR@EMBL-EBI
• RepeatMasker
• MUMmer (scan_for_match)
• Emboss Palindrome

Other nucleotide repeat finding methods found by a couple of web searches:

• Tandem Repeats Finder
• RECON
• RepeatRunner
• REPuter
• Imperfect Microsatellite Extractor (IMEx)
• Spectral Repeat Finder (SRF)
• REPFIND
• CRISPRfinder
• GrailEXP
• CONREPP
• find_palindromes
• Palindrome
• EMBOSS Palindrome
• Palindrome Search

Essential Qualification:

1. Master's degree in Bioinformatics / Computer Applications / Cognitive Science /Neuroscience/ Neuropsychology or equivalent. (Advantage will be given to NET JRF qualified candidate) Additional

Desirable Skills:

1) Programming skills (e.g., C++, Matlab, Python) 2) Experience/competent in working Window and Linux based programme.

Please mail your CV and covering letter to dr.uttam.kumar@gmail.com.

To know more about lab works please visit http://uttambrainlab.co.in/lab/.

Last date: 15/06/16

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Pay Scale : Rs. 32,500/-
How to apply
Candidates fulfilling these requirements should pre-register by sending their application in the prescribed format with recent CV and contact details of 2 referees by e-mail to ‘program.office@actrec.gov.in’ latest by 17.00 hrs on 23-06-2016. The interviews would be held on 27-06-2016 and only pre-registered candidates will be eligible to appear for interview. Candidates should report between 09.30 to 10.00 a.m. in Steno Pool, 3rd floor, Khanolkar Shodhika, ACTREC, Kharghar, Navi Mumbai.

More at http://www.actrec.gov.in/