BOL: Related items

Mulan: MUltiple sequence Local AligNment and conservation visualization tool

Rahul Nayak — Thu, 20 Jul 2017 08:02:32 -0500

Mulan performs multiple (2 or more) sequence alignments with an efficient and rapid "full local" alignment strategy that ensures a recapitulation of evolutionary sequence rearrangements (such as inversions and reshuffling) in any of the species. It combines refine and tba tools to align either "draft" or "finished" quality sequences. Mulan provides a dynamic graphical interface to align and visualize conservation profiles for evolutionarily distant and closely related species.

Input formats, automated data upload from the UCSC Genome Browser, gene annotation, annotation of repetitive elements, and progress report were previously described in the zPicture instructions and we refer the users to these materials for more details. This introduction is mainly focused on some novel features unique to the Mulan.

Address of the bookmark: https://mulan.dcode.org/mulanInstructions.php

SRF Vacancy at NIPGR

Tue, 25 Mar 2014 19:20:44 -0500

Applications are invited from suitable candidates for filling up the purely temporary position of one Senior Research Fellow in DST’s Indo-Australian Joint project (with ICRISAT) entitled “Genomic Approach for Stress Tolerant Chickpea” under the guidance of Dr. Mukesh Jain, Scientist, NIPGR.

(A) Senior Research Fellow (One Post): Emoluments as per DST/DBT norms.

Candidates having M.Sc. degree (with minimum of 55% marks) or equivalent in Life Sciences/Biotechnology/Bioinformatics/ Molecular Biology or any other related field with minimum of two years of post M.Sc. research experience are eligible to apply. The candidate having computer skill (Linux, Perl, Java, MySQL) and/or experience in advanced molecular biology, next generation sequencing data analysis and molecular markers analysis will be preferred.

The position is completely on temporary basis and co-terminus with the project. The initial appointment will be for one year, which can be curtailed/extended on the basis of assessment of the candidate’s performance and discretion of the Competent Authority. NIPGR reserves the right to select the candidate against the above posts depending upon the qualifications and experience of the candidates. Reservation of posts shall be as per Govt. of India norms.

Eligible candidates may apply by sending hard copy of completed application in the given format with a cover letter showing interest and attested copies of the certificates and proof of research experience. The applications should reach at the address given below within 15 days from the date of the advertisement. The subject line on envelope must be superscribed by “Application for the Post of SRF in DST - AISRF project”.

Note: ONLY hard copy of the application in the given format will be accepted.

Last date April 03, 2014

Dr. Mukesh Jain
Staff Scientist
National Institute of Plant Genome Research
Aruna Asaf Ali Marg, P.O. Box NO. 10531,
New Delhi - 110067

Advertisement: http://www.nipgr.res.in/careers/vacancies_latest.php#

ACANA: An accurate and consistent alignment tool for DNA sequences

Jit — Wed, 06 Dec 2017 09:45:29 -0600

ACANA is an accurate and consistent alignment tool for DNA sequences. ACANA is specifically designed for aligning sequences that share only some moderately conserved regions and/or have a high frequency of long insertions or deletions. It attempts to combine the best of local and global alignments algorithms in searching for evolutionarily related regions of sequences in order to achieve the best alignment. ACANA is also robust to the small changes of alignment parameters, particularly the gap extension score. As an accurate alignment tool, ACANA is particularly useful in comparative sequence analysis for identifying conserved functional regulatory elements.

Address of the bookmark: https://www.niehs.nih.gov/research/resources/software/biostatistics/acana/index.cfm

JUNIOR RESEARCH FELLOW POSITION at School of Biotechnology, Gautam Buddha University Greater Noida

Tue, 01 Apr 2014 14:46:57 -0500

Walk-In Interview for one position of Junior Research Fellow (JRF) in a SERB, Department of Science and Technology (DST) funded research project entitled “Design and evaluation of novel Beta-3 adrenoreceptor agonists for potential antidepressant activity” under the supervision of Dr. Shakti Sahi which was scheduled on 31st March, 2014 is now re-scheduled on account of public holiday.

The interview will now be held 01st April 2014. The monthly fellowship of JRF will be Rs 12,000/- plus HRA as per the University rules.

Essential Qualification: Master degree in any discipline of Life Science with NET qualified or valid GATE score.

Desirable Qualification: Preference will be given to candidates having research experience in Bioinformatics.

The interested candidates should report for the Interview on 01st April, 2014 at 10:00 am in the Conference Room of Dean, School of Biotechnology, First floor, Gautam Buddha University, Greater Noida. Interested candidates may also send their resume to undersigned by postmail/e-mail shaktis@gbu.ac.in or shaktisahi@gmail.com. No TA and DA will be paid for appearing for the interview.

Dr. Shakti Sahi
(Principle Investigator)
School of Biotechnology
Gautam Buddha University
Greater Noida
Ph:9971791897

www.gbu.ac.in/Recruitment/JRF_advertisement_DSTProject_Shakti_26March14.pdf

SMASH: An alignment-free tool to find and visualise rearrangements between pairs of DNA sequences

Jit — Thu, 21 Dec 2017 08:26:57 -0600

SMASH is a completely alignment-free method to find and visualise rearrangements between pairs of DNA sequences. The detection is based on relative compression, namely using a FCM, also known as Markov model, of high context order (typically 20). The method has been approached with a tool (also called SMASH). For visualization, SMASH outputs a SVG image, with an ideogram output architecture, where the patterns are represented with several HSV values (only value varies). The following image, illustrating the information maps between human and chimpanzee for the several chromosomes, depicts an example:

Address of the bookmark: https://github.com/pratas/smash

Postodoc in Computational/Systems Biology and Machine Learning

Wed, 09 Apr 2014 20:47:57 -0500

One profile of Computational/Systems Biology and Machine Learning at Postdoc level is needed at the Laboratory of Immunobiology of Neurological Disorders led by Cinthia Farina, Institute of Experimental Neurology, Ospedale San Raffaele, Milano. The projects of interest for this application involve research on translational bioinformatics in complex human disorders.

You have a PhD in Computational Science, Bioinformatics, or equivalent.

Especially relevant skills for the profile are:
1. In-depth understanding and implementation of methods and development of
algorithms for statistical and machine learning classification, clustering, predictive
modelling.
2. Experience on transcriptomics and clinical data analysis, in particular gene regulatory networks, protein interactomes, development of diagnostic tools.

3. Solid experience with data mining, bioinformatics programming and statistics for bioinformatics.
4. Flexibility and willing to work across multiple projects and technology in a rapidly evolving scientific context.

Candidates with programming/scripting experience are also welcome. In particular, proficiency in one or more mainstream programming languages (C, C++, Java, Python, Perl, etc.), together with the understanding of relational database design and SQL/DBMS systems (e.g. MySQL, PHP, Oracle).
Experience with the analysis of next-generation sequencing data is a plus.
Clear demonstration of experience in analysis and modelling of omics and clinical data must be provided.

Interested candidates should send to farina.cinthia@hsr.it:

1. CV (please show evidences of relevant titles, projects, courses, references, etc.)
2. One page with a list of research topics (i.e. ongoing projects)
3. earliest availability
4. 2-3 contact names

TAREAN: A computational tool for identification and characterization of satellite DNA from unassembled short reads

Surabhi Chaudhary — Tue, 15 May 2018 02:53:11 -0500

TAndem REpeat ANalyzer -TAREAN – is a computational pipeline for unsupervised identification of satellite repeats from unassembled sequence reads. The pipeline uses low-pass whole genome sequence reads and performs their graph-based clustering. Resulting clusters, representing all types of repeats, are then examined for the presence of circular structures and putative satellite repeats are reported.

How to use TAREAN:

Install a local instance of the pipeline using its source code available from bitbucket repository.
Use public Galaxy-based server at https://repeatexplorer-elixir.cerit-sc.cz/. The server is provided in frame of the Elixir CZ project and is maintained by CESNET and CERIT-SC. Simple registration is required to use this service.

Development of TAREAN was supported by ELIXIR CZ research infrastructure project (MEYS Grant No: LM2015047).

References

Novak, P., Avila Robledillo, L., Koblizkova, A., Vrbova, I., Neumann, P., Macas, J. (2017) – TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads. Nucleic Acids Res., doi:10.1093/nar/gkx257

Address of the bookmark: https://bitbucket.org/petrnovak/repex_tarean

Research Associate (RA) at INSTITUTE OF ADVANCED STUDY IN SCIENCE AND TECHNOLOGY

Mon, 05 May 2014 08:44:24 -0500

INSTITUTE OF ADVANCED STUDY IN SCIENCE AND TECHNOLOGY
(An Autonomous Institute under Department of Science and Technology, Govt. of India)
Paschim Boragaon, Garchuk, Guwahati-781035

Appointment Adv.No.2

Applications in plain paper are invited from Indian citizens for one/two position each of Research Associate, Traineeship and Studentship for BIF facility, Division of Life Sciences, IASST.

Applications with complete Bio-data containing contact address, e-mail and phone number, two recent passport size photographs and attested copies of mark sheets, certificates etc., should be sent to the Registrar, IASST, Paschim Boragaon, Garchuk, Guwahati – 781035, Assam, so as to reach on or before 5/05/2014.

A. Research Associate:

Number of vacancies: 1 (One)

Qualifications:

PhD in Bioinformatics or allied disciplines with knowledge of Bioinformatics. The candidates who have submitted PhD thesis may also apply.

In case, candidates having PhD are not found, candidates having MSc in Bioinformatics or allied disciplines with sound knowledge of Bioinformatics will be preferred.

Remuneration: Candidate having PhD will get a consolidated remuneration of Rs. 22,000/- +HRA per month. MSc having NET/GATE/SLET qualified candidate will get a remuneration of Rs. 16,000/= and HRA and candidate with only MSc will get a remuneration of Rs.14,000/- and HRA.

Tenure:

The post is initially for one year and may be extended depending on the performance till the tenure of the project.

B. Traineeship:

Number of vacancies: 2 (Two)

Qualifications:

Candidate with a postgraduate degree in Bioinformatics/Biotechnology/Life sciences from a recognised University

Remuneration: Rs. 5000/month for 6 months

C. Studentship:

Number of vacancies: 2 (Two)

Qualifications:

Candidate pursuing M.Sc in bioinformatics in a recognised University.

Remuneration: Rs. 5000/month for 6 months

http://iasst.gov.in/pdf/recruitment/advt%20no_2_24042014.pdf

“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files

Poonam Mahapatra — Mon, 04 Jun 2018 03:45:15 -0500

One code to find them all is a set of perl scripts to extract useful information from RepeatMasker about transposable elements, retrieve their sequences and get some quantitative information. Assemble RepeatMasker hits into complete TE copies, including LTR-retrotransposon Retrieve corresponding TE sequences, and flanking sequences, from the local fasta files Compute summary statistics for each TE family (number of TE copies, genome coverage...) Ambiguous cases such as nested TE can be assembled into copies automatically or manually Allow for working with a TE user-defined library Allow for working with only a user-chosen set of TE families http://doua.prabi.fr/software/one-code-to-find-them-all

Address of the bookmark: http://doua.prabi.fr/software/one-code-to-find-them-all

“On” and “Off” the neuron !!!

Rahul Nayak — Fri, 25 Apr 2014 19:31:13 -0500

Optogenetics is a recent innovation in neuroscience that gives researchers the ability to control the activity of neurons with light. With this powerful tool, researchers are teasing apart the biological basis of memory, behavior, and disease (see “Scientists Make Mice ‘Remember’ Things That Didn’t Happen” and “An On-Off Switch for Anxiety,”). But for the first several years of this technology’s existence, the proteins that scientists added to neurons to make them react to light were only good at activating neurons. That limited researchers’ ability to understand neuronal circuits, sets of interconnected neurons that are thought to control behavior and, when misfiring, to underlie many brain conditions. Problems can arise from any imbalance in circuit activity, whether too much or too little.

Now, two research groups have engineered new optogenetic proteins that can be used to efficiently silence neurons. One of the two new proteins comes from the lab of Karl Deisseroth, a psychiatrist and neuroscientist at Stanford University who helped develop optogenetics as a research tool. His group’s new “off” switch for neurons was created by changing 10 of the 333 amino acids in an existing optogenetic protein, which itself had been engineered by combining natural proteins from green algae. That advance “creates a powerful tool that allows neuroscientists to apply a brake in any specific circuit with millisecond precision,” said Thomas Insel, director of the National Institute of Mental Health, in a released statement. The other new silencing protein, developed by scientists at the Humboldt University of Berlin and collaborators, was created by changing amino acids in the same existing optogenetic protein.

Some researchers are also looking to optogenetics as a potential treatment for patients with a variety of conditions (see “For Mice, and Maybe Men, Pain Is Gone in a Flash,” and “Flipping on the Lights to Halt Seizures”) but there are huge challenges to overcome. The method requires genetic modification of cells to make them light-sensitive. It also requires implanted light sources for all but the shallowest of nerve endings.