BOL: Related items

ORFfinder with smart BLAST

Jit — Tue, 17 May 2016 01:43:15 -0500

ORF Finder

ORFfinder is a graphical analysis tool for finding open reading frames (ORFs). We’ve been working on a few updates, and we’d like to find out what you think about them. Read on to find out what you can do with the new ORFfinder.

Smart BLAST (https://ncbiinsights.ncbi.nlm.nih.gov/2015/07/29/smartblast/)

Select one or a group of ORFs and BLAST several databases at once, and use the newly developed SmartBLAST to verify protein names. Looking for the traditional results from BLAST? They’re there too.

MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping

Neel — Fri, 20 May 2016 18:53:49 -0500

MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align reads generated by all the major sequencing technologies, including Illumina, Applied Biosystems SOLiD, Roche 454, Ion Torrent and Pacific BioSciences SMRT. Indeed, MOSAIK was the only aligner to provide consistent mappings for all the generated data (sequencing technologies, low-coverage and exome) in the 1000 Genomes Project. To provide highly accurate alignments, MOSAIK employs a hash clustering strategy coupled with the Smith-Waterman algorithm. This method is well-suited to capture mismatches as well as short insertions and deletions. To support the growing interest in larger structural variant (SV) discovery, MOSAIK provides explicit support for handling known-sequence SVs, e.g. mobile element insertions (MEIs) as well as generating outputs tailored to aid in SV discovery.

Address of the bookmark: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0090581

Senior Project Fellow Bioinformatics at NBRI

Sat, 21 May 2016 21:01:05 -0500

Walk In Interview No. 03/Project/2016
Senior Project Fellow Bioinformatics Job vacancies in CSIR- National Botanical Research Institute (NBRI), Lucknow
Area III: Molecular Biology & Biotechnology
Qualification : 1st Class M.Sc. in Bioinformatics/Biotechnology/ Life Science /Biochemistry/Botany with 2 years research experience and at least one publication in SCI Journal or 1st class M.Tech in Bioinformatics
Age : 32 years
Salary : Rs.18000
How to apply
Date & Venue of Interview For Area III: 27-05-2016 at 11.00 A.M. at Conference Room, T.N. Khushoo Block, NBRI, Lucknow.

http://www.nbri.res.in/temp.php

Research Associate Bioinformatics at MANIT

Thu, 26 May 2016 02:20:58 -0500

Research Associate Jobs opportunity in Maulana Azad National Institute of Technology (MANIT) on contract basis
Project : “Screening of Anti-venom potential of medicinal plants from Tribal region of Madhya Pradesh"
No. of Post : 01

Qualification : The minimum qualifications are : Ph.D in Bioinformatics/ Biotechnology or allied branches with atleast two publication in SCI journals.
Fellowship : The consolidated emoluments of Rs.36, 000/ PM+HRA+MA as per CSIR rules.

How to apply
Applications (in prescribed attached format and supporting documents) to be received in the Dr. Rahul Shrivastava, Principal Investigator (CSIR Project), Department of Biological Science and Engineering, Maulana Azad National Institute of Technology, Bhopal – 462003 (MP) on or before 7th June 2016.

More at http://www.web.manit.ac.in/Year%202016/Recruitment%20Contract%20Faculty/Biological/Advertisement%20for%20Antivenome%20project%202.pdf

BioDBnet

Jit — Thu, 02 Jun 2016 11:11:47 -0500

Database to Database Conversions

db2db allows for conversions of identifiers from one database to other database identifiers or annotations. To use db2db select the input type of your data, changing the input type automatically changes the output options to the ones specific for the input selected. Then select one or more output types and add your identifiers in the ID list box. Set the remove duplicate values to 'No' if you do not want duplicates to be removed. Clicking on submit then returns a table of your inputs matched against all the outputs selected in the exact order as entered. Results can be limited to a particular taxon by entering it's Taxon ID. The performance will vary widely depending on the number of outputs and the options selected. Conversions to a single output with the default options should complete in a few seconds

Address of the bookmark: https://biodbnet-abcc.ncifcrf.gov/db/db2db.php

Assistant Professor Bioinformatics / Teaching Assistant at Gujarat University

Sat, 04 Jun 2016 16:04:26 -0500

Assistant Professor Bioinformatics / Teaching Assistant Jobs recruitment in Gujarat University
Departments :

M.Sc. Bioinformatics Climate Change and Impacts Management
M.Sc. Biotechnology and Clinical Research

Department of Computer Science (Rollwala Computer Centre)
Appointment will be on purely contract basis for 11 months on consolidated salary. Reservation as per rules

How to apply
All the candidate are here by required to fill up the application form and given to concern Department, Gujarat University, Ahmedabad (Form can be submitted personally or thorough post/courier.) Candidates are supposed to attach the self attested photocopies of their required testimonials along with application form. Last date of receipt of application is 10/06/2016.

More http://www.gujaratuniversity.org.in/web/NWD/NewsEvents/1700_Recruitments%20at%20Gujarat%20University.asp

Blobsplorer

Jit — Tue, 14 Jun 2016 10:28:58 -0500

Blobsplorer is a tool for interactive visualization of assembled DNA sequence data ("contigs") derived from (often unintentionally) mixed-species pools. It allows the simultaneous display of GC content, coverage, and taxonomic annotation for collections of contigs with a view to separating out those belonging to different taxa.

Blobsplorer is unlikely to be of use on its own as it requires contig data to be supplied in a format that involves considerable preprocessing (see below for a description). The easiest way to use Blobsplorer is as part of a workflow using scripts from here.

Address of the bookmark: http://nematodes.org/martin/blobsplorer/blobsplorer.html

CNIDARIA: fast, reference-free phylogenomic clustering

Shruti Paniwala — Thu, 16 Jun 2016 17:55:17 -0500

Motivation: Identification of biological specimens is a major requirement for a range of applications. Reference-free methods analyse unprocessed sequencing data without relying on prior knowledge, but these do not scale to arbitrarily large genomes and arbitrarily large phylogenetic distances.

Results: We present Cnidaria, a practical tool for clustering genomic and transcriptomic data with no limitation on ge-nome size or phylogenetic distances. We successfully simultaneously clustered 169 genomic and transcriptomic datasets from 4 kingdoms, achieving 100% accuracy at supra-species level and 78% accuracy for species level.

Availability and Implementation: Cnidaria is written in C++ and Python and is available at http://www.ab.wur.nl/cnidaria.

Contact: Saulo Aflitos - sauloal@gmail.com

Supplementary information: Supplementary data are available at Bioinformatics online.

Address of the bookmark: https://github.com/sauloal/cnidaria/wiki

Greengenes database

Jit — Wed, 29 Jun 2016 10:03:31 -0500

The greengenes web application provides access to the 2011 version of the greengenes 16S rRNA gene sequence alignment for browsing, blasting, probing, and downloading. The data and tools presented by greengenes can assist the researcher in choosing phylogenetically specific probes, interpreting microarray results, and aligning/annotating novel sequences. If you are an ARB user, you can use greengenes to keep your own local database current.

Address of the bookmark: http://greengenes.lbl.gov/cgi-bin/nph-index.cgi

SRF/ Project Assistant Bioinformatics at NIRRH

Sun, 19 Jun 2016 09:11:13 -0500

SRF/ Project Assistant Bioinformatics recruitment in National Institute for Research in Reproductive Health (NIRRH)

Title of Project : 1. “Analysis Of The Structures Of Known Antimicrobial Peptides Using Machine Learning Algoitms And Molecular Dynamics Simulations”

Senior Research Fellow /1 Post

Qualification: First class M.Sc. in Bioinformatics/ Biological Sciences from recognized university with 2 years research experience and CSIR/UGC/ICMR net qualified OR First class M.Sc. in Bioinformatics/ Biological Sciences from recognized university with 2 years research experience Research experience in bioinformatics and wetlab methods.

Age: Not exceeding 35 Years

Pay Scale : Rs.18,000/- + 30% HRA Rs.14,000/- + 30% HRA

Project Assistant (Level-II) /1 Post

Qualification: First class M.Sc. in Bioinformatics/ Biological Sciences/Computer Sciences Training experience in bioinformatics and wetlab methods .

Age: Not exceeding 28 Years

Pay Scale : Rs.8,000
How to apply
Candidates must bring along with them all the relevant documents in original and one set of attested photocopies of the same and one passport size recent colour photograph.

Walk-in-Interview on 28.06.2016 between 09:00 hrs. to 12:00 hrs.

More at http://www.nirrh.res.in/links/job_oppotunities.htm