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

Stand-alone programs for Bioinformatician

Radha Agarkar — Sat, 21 May 2016 22:50:15 -0500

This directory contains applications for stand-alone use, built specifically for a Linux 64-bit machine.

For help on the bigBed and bigWig applications see:
http://genome.ucsc.edu/goldenPath/help/bigBed.html
http://genome.ucsc.edu/goldenPath/help/bigWig.html

View the file 'FOOTER' to see the usage statement for each of the applications.

Address of the bookmark: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/

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

MutaBind

Jit — Mon, 06 Jun 2016 13:34:09 -0500

MutaBind is a new computational method and server created through NCBI research efforts that maps mutations on a protein structural complex, calculates changes in binding affinity, identifies deleterious mutations and produces a downloadable mutant structural model. http://www.ncbi.nlm.nih.gov/projects/mutabind/index.fcgi/

MutaBind guides you through this process, step by step, starting with selecting a protein complex and inputting PDB code or uploading PDB files. You can also retrieve results with a job ID number, view help documents, and review the MutaBind method and references.

More at http://www.ncbi.nlm.nih.gov/projects/mutabind/index.fcgi/

Guest Faculty Centre for Bioinformatics at Pondicherry University

Wed, 15 Jun 2016 03:44:31 -0500

Guest Faculty Centre For Bioinformatics Jobs opportunity in Pondicherry University
Qualification : M.Phil. (with NET/SLET)/ M.Tech. / M.E. in Computer Science with a minimum of 55% of marks as per UGC norms.
Desirable : Ph.D and Teaching experience in Perl and Java programming.
Honorarium : Rs. 1,000/- per lecture (subject to a maximum of Rs. 25,000/- per month)
How to apply
Walk-in-Interview will be held on 29.06.2016 (Wednesday) at 2:30 P.M at the office of Centre for Bioinformatics, Pondicherry University, Puducherry — 605 014. Interested eligible candidates may attend the Walk-in-Interview along with all original certificates, self attested photocopies and testimonials with a copy of their bio-data. Candidates reporting after 2:30 P.M will not be entertained.

More at http://www.pondiuni.edu.in/news?quicktabs_2=5#quicktabs-2

clusterProfiler

Jit — Thu, 16 Jun 2016 18:57:03 -0500

statistical analysis and visulization of functional profiles for genes and gene clusters

Bioconductor version: Release (3.3)

This package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene and gene clusters.

Author: Guangchuang Yu with contributions from Li-Gen Wang and Giovanni Dall'Olio.

Maintainer: Guangchuang Yu

Citation (from within R, enter citation("clusterProfiler")):

Yu G, Wang L, Han Y and He Q (2012). “clusterProfiler: an R package for comparing biological themes among gene clusters.” OMICS: A Journal of Integrative Biology, 16(5), pp. 284-287.
Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("clusterProfiler")

https://www.bioconductor.org/packages/devel/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html

Address of the bookmark: https://www.bioconductor.org/packages/devel/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html

Research Assistant Bioinformatics at Andhra University

Sat, 18 Jun 2016 18:39:09 -0500

Advt. No. AUMLR/BIF/ RA /6-2016
Research Assistant Job Position in Andhra University on temporary basis
No. of Post : 01
Eligibility : Applicants who have completed their Post Graduate degree in Bioinformatics.
Desirable : Undergone traineeship in BIF; at least one publication in Bioinformatics.
Stipend : A monthly stipend of Rs. 22,000/- + HRA (HRA is applicable only for NET qualified candidates)
How to apply
Applications on plain paper, stating the name, address, date of birth, educational qualifications and experiences, and Institute, along with attested photocopies of mark sheets and certificates, should be submitted to K. UMADEVI, Coordinator, BIF Programme, Department of Marine Living Resources, Andhra University, Visakhapatnam-530 003, Andhra Pradesh, on or before 15th July, 2016.

Candidates are required to appear for an interview, with all the necessary certificates in original along with a set of attested copies in the office of the Principal, AU College of Science & Technology, Andhra University, Visakhapatnam. Applications may be sent by Email to andhrauniv.btisnet@nic.in / katruumadevi@gmail.com.