At the Repository for Tomato Genomics Resources, we are working on Tomato Functional Genomics, using TILLING, Insertional Mutagenesis, proteomics, metabolomics approaches to study fruit ripening in tomato. The current aims of the group include using reverse and forward genetics strategies to isolate tomato mutants delayed in ripening, having high lycopene and folate content in tomato fruits and analysis of light and hormonal signal transduction pathways. For recent publications of the group see (Plant Physiol 161: 2085–2101, Plant Physiol 156: 1424-1438; Molecular Plant 3: 854-869; Plant Methods 6: 3; Plant Methods 5:18; Plant Signaling and Behavior 5:11.).

Currently we have one position available in the projects awarded to Prof. R.P. Sharma funded by Dept of Biotechnology. The qualification for this Position is as follows:

Research Assistant: Applicants should have experience in networking using R language and should be able to develop networks using the transcriptome, proteome and metabolite data sets. M.Tech. in Bioinformatics is required. The selected candidate would be paid Rs. 13,000/-pm- consolidated.

Candidates interested in above positions should send a one page statement clearly explaining how their skills are relevant to the position. The candidates should also enclose detailed CV and the name/email id for three referees. The candidates can send their application by email at rameshwar.sharma@uohyd.ac.in and y.sreelakshmi@uohyd.ac.in on or before December 10th, 2013. The position is purely temporary in nature. Shortlisted candidates would be called for interview. No TA/DA would be provided for attending the interview. We also have openings for CSIR-NET JRF candidates for pursuing PhD in above research areas.

Interested candidates with CSIR-NET JRF can send their CV to the above email
addresses.

Advertisement:

http://www.uohyd.ac.in/images/recruitment/tomanet_positions_221113.pdf

"Computational Methods for the Analysis of the Diversity and Dynamics of Genomes"

has currently open positions for graduate students, to study at Simon Fraser University (Vancouver, Canada) and
Bielefeld University (Germany), starting in the fall 2014.

This international graduate program is a close cooperation of:

Bielefeld University, Germany: Graduate progam "DiDy"
Simon Fraser University (SFU), Vancouver, Canada: Graduate program "MADD-Gen"

The available positions include six PhD positions at Bielefeld University, as well as PhD and MSc positions at SFU.

Application deadline: December 31st, 2013
Webpage: http://wiki.techfak.uni-bielefeld.de/didy/Announcement

Highlights of our research include:

Optimization of microarray design, probe signal interpretation
Advanced models and tools for expression profiling
State-of-the-art applications and integrated analyses

Lab page @ http://bioinf.boku.ac.at/

Apply to Genotypic Technology if you are a PhD in Life Sciences/ Molecular Biology/ Biotechnology/ Human Genetics/ Bioinformatics with minimum 4-5 years post doctoral experience as well as publications in peer reviewed journals.

Source: http://www.genotypic.co.in/Careers/2/Current-Openings.aspx

Translational recoding.

RNA editing.

Evolution of the genetic code and translation.

More at http://lapti.ucc.ie/research.html

Lab page http://lapti.ucc.ie/index.html

• Bioconductor – A plethora of tools for analysis and comprehension of high-throughput genomic data, including 1500+ software packages. [ paper-2004 | web ]
• Biopython – Freely available tools for biological computing in Python, with included cookbook, packaging and thorough documentation. Part of the Open Bioinformatics Foundation. Contains the very useful Entrez package for API access to the NCBI databases. [ paper-2009 | web ]
• Bioconda – A channel for the conda package manager specializing in bioinformatics software. Includes a repository with 3000+ ready-to-install (with conda install) bioinformatics packages. [ paper-2018 | web ]
• BioJulia – Bioinformatics and computational biology infastructure for the Julia programming language. [ web ]
• Rust-Bio – Rust implementations of algorithms and data structures useful for bioinformatics. [ paper-2016 ]
• SeqAn – The modern C++ library for sequence analysis.

Name of the fellowship: Junior Research Fellow (JRF) / Project Fellow

Title of the project: Genome-wide Mapping of Murine Specific Dengue T-cell Epitopes: Computational Prediction, Identification and use as Candidate Vaccines

Duration: 3 years

Fellowship: Rs. 18,000 for first 2 years and Rs. 20,000 for 3rdyear (for M.Tech. candidates)

Rs. 16,000 for first 2 years and Rs. 18,000 for 3rdyear (for M.Sc. candidates with NET qualification)

Rs. 8,000 for first 2 years and Rs. 10,000 for 3rdyear (for M.Sc. candidates without NET qualification)

Qualifications: M.Tech. in Biotechnology / M.Sc. in any branch of Life Sciences

Desirable Experience: Minimum of two years research experience in any of the following areas: Immunology / Microbiology / Gene Manipulation / Bioinformatics

Interested and eligible candidates may apply with their resume along with relevant documents and a passport size photograph to the Principal Investigator by post (or e-mail) on or before December 31, 2013. Only short listed candidates will be called for written test and/or interview. Selected candidate may register for PhD in Kalasalingam University. No TA/DA will be paid for attending interview.

Dr. K. Sundar
Principal Investigator (SERB Project)
Department of Biotechnology
Kalasalingam University
Krishnankoil – 626126, Tamil Nadu
sundarkr@klu.ac.in

Established by Government of Rajasthan

Approved by UGC under Sec 2(f) of UGC Act 1956

ADVERTISEMENT FOR FACULTY POSITION AT JAIPUR NATIONAL UNIVERSITY,JAIPUR

Jaipur National University, Jaipur is a premier centre of learning, providing various integrated and interdisciplinary programmes of study and research in the country. With the opening of the School of Distance Education & Learning, JNU has taken education to the doorsteps of those aspirants who, for some reason, could not be a part of regular stream of education. In this era of competition & ambition for excellence, it has become imperative to have quality education & an alert mind coupled with the right attitude to carry onself, and for this, JNU happens to be the most sought after destination.

School Of Life Sciences: Bioinformatics, Chemistry

Total no of Post: 04

Education:

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PG – M.Sc /M.Tech Chemistry

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Website: http://www.jnujaipur.ac.in

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Email Address: dsbhatia5@yahoo.com

Ph:, +917568246839

• the Damerau–Levenshtein distance allows insertion, deletion, substitution, and the transposition of two adjacent characters;
• the longest common subsequence (LCS) distance allows only insertion and deletion, not substitution;
• the Hamming distance allows only substitution, hence, it only applies to strings of the same length.
• the Jaro distance allows only transposition.

use Text::Levenshtein qw(distance);

 print distance("foo","four");
 # prints "2"

 my @words     = qw/ four foo bar /;
 my @distances = distance("foo",@words);

 print "@distances";
 # prints "2 0 3"

use Algorithm::LCSS qw( LCSS CSS CSS_Sorted );
    my $lcss_ary_ref = LCSS( \@SEQ1, \@SEQ2 );  # ref to array
    my $lcss_string  = LCSS( $STR1, $STR2 );    # string
    my $css_ary_ref = CSS( \@SEQ1, \@SEQ2 );    # ref to array of arrays
    my $css_str_ref = CSS( $STR1, $STR2 );      # ref to array of strings
    my $css_ary_ref = CSS_Sorted( \@SEQ1, \@SEQ2 );  # ref to array of arrays
    my $css_str_ref = CSS_Sorted( $STR1, $STR2 );    # ref to array of strings

There are many different modules on CPAN for calculating the edit distance between two strings. Here's just a selection.

Text::LevenshteinXS and Text::Levenshtein::XS are both versions of the Levenshtein algorithm that require a C compiler, but will be a lot faster than this module.

The Damerau-Levenshtein edit distance is like the Levenshtein distance, but in addition to insertion, deletion and substitution, it also considers the transposition of two adjacent characters to be a single edit. The module Text::Levenshtein::Damerau defaults to using a pure perl implementation, but if you've installed Text::Levenshtein::Damerau::XS then it will be a lot quicker.

Text::WagnerFischer is an implementation of the Wagner-Fischer edit distance, which is similar to the Levenshtein, but applies different weights to each edit type.

Text::Brew is an implementation of the Brew edit distance, which is another algorithm based on edit weights.

Text::Fuzzy provides a number of operations for partial or fuzzy matching of text based on edit distance. Text::Fuzzy::PP is a pure perl implementation of the same interface.

String::Similarity takes two strings and returns a value between 0 (meaning entirely different) and 1 (meaning identical). Apparently based on edit distance.

Text::Dice calculates Dice's coefficient for two strings. This formula was originally developed to measure the similarity of two different populations in ecological research.