BOL: Related items

WALK-IN-INTERVIEW for the post of JRF and Project Assistant @ CIFT

Tue, 20 Jan 2015 23:03:20 -0600

Eligible candidates are invited to attend a walk-in-Interview with all relevant documents for the following positions of Project Fellows (on contractual basis) to work in the Project “ Genetic Diversity of Clostridium botulinum in seafood and Development of Lateral Flow Immuno Assay (LFIA) for toxinotyping funded by Department of Biotechnology. The duration of the project is 3 years / co-terminus with the scheme.

Jr. Research Fellow – 2 posts

Fellowship : Rs. 25000/- + 20% HRA pm for Ist & 2nd year and Rs.28000/- + HRA on 3rd year

Qualification : Ist class Masters Degree in Microbiology/Fishery Microbiology/Bio-technology.

Desirable :

1. CSIR/UGC NET/JRF qualified

2. Excellent analytical skills and computer documentation

3. Prior experience in handling microbial cultures and molecular techniques

Project Assistant – 1 post

Fellowship : Rs.8000/- p.m (consolidated)

Qualification: Masters degree in Microbiology/Biotechnology with skill in Bioinformatics

Desirable: Excellent analytical skills in Bioinformatics and computer documentation

Terms & Conditions:

Registration will begin at 8.30 a.m and will close at 11.00 am
Age limit (as on 29.1.2015): Below 35 years for men and 40 years for women.
Age relaxation of 3 year for OBC candidates and 5 years for SC/ST candidates is permissible.
Candidates are required to submit self-attested copies of all the Certificates in support of their claims regarding age, educational qualifications, scheduled caste/scheduled tribe/OBC etc. The original certificates shall be produced for verification before the interview.
Candidates should bring detailed bio-data (in the enclosed format) affixing a recent passport size photograph.
The selected candidate will be recruited on contract basis under ICAR norms. The post is purely temporary and is co-terminus with the project.
The candidates attending the interview should ensure that they fulfil all the eligibility conditions. No correspondence will be entertained from the candidates for selection/test/appointment.
No TA/DA will be paid to attend the interview.
Canvassing in any form will render the candidate disqualified for the post.
The Director’s decision will be final and binding in all aspects regarding the selection to the post.

Venue: CIFT, Matsyapuri.P.O, Cochin Date of interview: 29.01.2015 Time: 10.00 am

http://www.cift.res.in/uploads/userfiles/file/file/srf%20appn.doc

TelomereHunter

Jit — Fri, 02 Feb 2018 04:23:59 -0600

TelomereHunter is a tool for estimating telomere content from human whole-genome sequencing data. It is designed to take BAM files from a tumor and a matching control sample as input. However, it is also possible to run TelomereHunter with one input file. TelomereHunter extracts and sorts telomeric reads from the input sample(s). For the estimation of telomere content, GC biases are taken into account. Finally, the results of TelomereHunter are visualized in several diagrams.

TelomereHunter is available for download at the following address: https://pypi.python.org/pypi/telomerehunter/

Address of the bookmark: http://www.dkfz.de/en/applied-bioinformatics/telomerehunter/telomerehunter.html

WALK-IN-INTERVIEW FOR PROJECT ASSISTANT @ BHARATHIDASAN UNIVERSITY

Mon, 12 Jan 2015 21:54:10 -0600

BHARATHIDASAN UNIVERSITY
DEPARTMENT OF BIOINFORMATICS, SCHOOL OF LIFE SCIENCES, TIRUCHIRAPPALLI – 620024

Project title: “Genome-scale metabolic modeling and simulation of rumen methanogens An in silico attempt to methane attenuation”

Funding Agency: University Grants Commission, New Delhi

Tenure of the project: Two years or till the end of the project period.

Position: Project Assistant (1 no.)

Essential qualification: First class M.Sc. in Bioinformatics/Microbiology/ Biotechnology and other related discipline.

Desirable qualification: Experience in an area relevant (Molecular Systems Engineering) to the project.

Fellowship: Rs. 5000 per month as per the UGC norms.

Upper age limit: 28 years

Date of Venue of interview: 22.01.2015, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli -620 024, Tamil Nadu

The above post is purely temporary and will be terminated with three month notice.

The Terms and the condition of the appointment shall be governed according to UGC, Govt. of India. The eligible candidates will bring their original certificates and documents at the time of interview. No TA/DA will be paid for attending the interview.

Dr. P. CHELLAPANDI
UGC-Research Awardee,
Department of Bioinformatics,
School of Life Sciences,
Bharathidasan University,
Tiruchirappalli -620 024, Tamil Nadu

Advertisement: www.bdu.ac.in/adv/PA_UGC_Bioinformatics.pdf

HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads

Rahul Nayak — Tue, 08 May 2018 04:27:22 -0500

HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Based on an extension of BWT for graphs [Sirén et al. 2014], we designed and implemented a graph FM index (GFM), an original approach and its first implementation to the best of our knowledge. In addition to using one global GFM index that represents a population of human genomes, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome (each index representing a genomic region of 56 Kbp, with 55,000 indexes needed to cover the human population). These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. This new indexing scheme is called a Hierarchical Graph FM index (HGFM).

more at https://ccb.jhu.edu/software/hisat2/index.shtml

Address of the bookmark: https://github.com/infphilo/hisat2

Linux operating system aimed at scientists

Pranjali Yadav — Mon, 19 Jan 2015 08:30:49 -0600

The Bio-Linux operating system is based on Ubuntu 14.04 LTS (Trusty Tahr), and the previous version was using Ubuntu 12.04 LTS. The developers only use LTS releases and that means that upgrades for this distro don't come along all that often.

This Linux distribution is aimed at scientists and it comes with more than 250 bioinformatics packages, 50 graphical applications and several hundred command line tools. And this is just skimming the surface of what the OS can do. Users have access to even more apps from the official repositories.

Bio-Linux is using an Ubuntu LTS version as its base

The fact that it uses Ubuntu LTS versions for the base is a good thing because it means its users won't have to worry about the support. Ubuntu 14.04 LTS is supported until 2019, so people who are using Bio-Linux shouldn't have a problem.

"An updated Bio-Linux 8 version is now on the website in ISO and OVA versions. As usual, there is no need to download this version if you are an existing user. All updates to existing packages will be applied to your system through the update manager and new packages are all available via apt-get or Synaptic," reads the announcement.

The changelog also states that a problem that was preventing the desktop to not start on VirtualBox has been fixed, the QIIME and Bowtie-Bio tools have been upgraded, the pandaseq paired end assembler has been added, and the beginners tutorial specific to Bio-Linux 8 has been improved.

Check out the official announcement for a complete list of changes and updates. You can download Bio-Linux 8.0.5 right now from Softpedia and give it a spin. It has the Unity desktop and now it runs very well in virtual environments.

Reference @ http://news.softpedia.com/news/Bioinformatics-Distro-Bio-Linux-8-0-5-Now-Available-for-Download-469867.shtml

BlasR Mapping single molecule sequencing reads using Basic Local Alignment with Successive Refinement (BLASR): Theory and Application,

Jit — Wed, 23 May 2018 06:54:32 -0500

BLASR (Basic Local Alignment with Successive Refinement) for mapping Single Molecule Sequencing (SMS) reads that are thousands to tens of thousands of bases long with divergence between the read and genome dominated by insertion and deletion error.

Here is how I use the blasr to align PacBio reads to the contigs (target.fasta). The “target.fasta.sa” is the suffix array from “target.fasta” generated by sawriter.

blasr query.fa ./target.fasta -sa ./target.fasta.sa -bestn 40 -maxScore -500 -m 4 -nproc 24 -out target.m4 -maxLCPLength 15

the output format option “-m 4″ generate the alignment coordinate. Not fully documented, but I can explain that to you.

I use a 24 cores / 48G ram server for the alignment. It took about 2 to 3 hours aligning 3G PacBio Reads to 10^6 sequences of short read contigs with a mean 3.5kbp length.

Address of the bookmark: http://bix.ucsd.edu/projects/blasr/

DNA Transcription (Advanced)

Thu, 29 Jan 2015 05:31:42 -0600

Transcription is the process by which the information in DNA is copied into messenger RNA (mRNA) for protein production. Originally created for DNA Interactive ( http://www.dnai.org ). TRANSCRIPT: The Central Dogma of Molecular Biology: "DNA makes RNA makes protein" Here the process begins. Transcription factors assemble at a specific promoter region along the DNA. The length of DNA following the promoter is a gene and it contains the recipe for a protein. A mediator protein complex arrives carrying the enzyme RNA polymerase. It manoeuvres the RNA polymerase into place... inserting it with the help of other factors between the strands of the DNA double helix. The assembled collection of all these factors is referred to as the transcription initiation complex... and now it is ready to be activated. The initiation complex requires contact with activator proteins, which bind to specific sequences of DNA known as enhancer regions. These regions may be thousands of base pairs distant from the start of the gene. Contact between the activator proteins and the initiation-complex releases the copying mechanism. The RNA polymerase unzips a small portion of the DNA helix exposing the bases on each strand. Only one of the strands is copied. It acts as a template for the synthesis of an RNA molecule which is assembled one sub-unit at a time by matching the DNA letter code on the template strand. The sub-units can be seen here entering the enzyme through its intake hole and they are joined together to form the long messenger RNA chain snaking out of the top.

ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data

Rahul Nayak — Tue, 03 Jul 2018 04:14:52 -0500

ChopStitch is a new method for finding putative exons and constructing splice graphs using an assembled transcriptome and whole genome shotgun sequencing (WGSS) data. ChopStitch identifies exon-exon boundaries in de novo assembled RNA-seq data with the help of a Bloom filter that represents the k-mer spectrum of WGSS reads. The algorithm also detects base substitutions in transcript sequences corresponding to sequencing or assembly errors, haplotype variations, or putative RNA editing events. The primary output of our tool is a FASTA file containing putative exons. Further, exon edges are interrogated for alternative exon-exon boundaries to detect transcript isoforms, which are reported as splice graphs in dot output format.

Address of the bookmark: https://github.com/bcgsc/ChopStitch

RA Bioinformatics at CIBA

Mon, 02 Feb 2015 22:52:50 -0600

The following posts are to be filled purely on temporary basis under CIBA Component of “Centre for Agricultural Bioinformatics (CABin)” project at this Institute.

Research Associate – one post

Date & Time of Interview 18th Feb 2015 at 10.00 a.m.

Essential Qualification Ph.d / M.Sc./ M.Phil (Bioinformatics) With 1st division or 60% marks or equivalent overall grade point average with at least two years of research experience in the relevant subject.

Desirable qualification: Experience in Java/ C++/ PHP/ PERL/ Python etc. based application development using Linux, Apache and MySQL/Oracle.

Emoluments Rs.24000/- p.m. + 30% HRA for Ph.D holders / Rs.23000/- p.m. + 30% HRA for Master Degree holders A consolidated pay Rs.25000/- per month.

Age Limit Maximum 40 years for men and 45 years for women as on date of interview. Age limits are relaxable for SC / ST / OBC candidates as per rules. Maximum 40 years for men and 45 years for women as on date of interview. Age limits are relaxable for SC / ST / OBC candidates as per rules.

Eligible Candidates may appear for the Walk-in-interview with original Certificate of Ph.D. / Master’s / relevant degree, passport size photograph and bio-data enclosing attested copies of educational qualification & experience certificates. TA / DA will not be paid for attending the interview.

Advertisement: www.ciba.res.in/attachments/jobs/CABin-3006.pdf

PureCN: copy number calling and SNV classification using targeted short read sequencing

Jit — Thu, 09 Aug 2018 04:09:37 -0500

This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with standard somatic variant detection and copy number pipelines, and has support for tumor samples without matching normal samples.

Author: Markus Riester [aut, cre], Angad P. Singh [aut]

Maintainer: Markus Riester

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

Riester M, Singh A, Brannon A, Yu K, Campbell C, Chiang D, Morrissey M (2016). “PureCN: Copy number calling and SNV classification using targeted short read sequencing.” Source Code for Biology and Medicine, 11, 13. doi: 10.1186/s13029-016-0060-z.

Address of the bookmark: http://bioconductor.org/packages/release/bioc/html/PureCN.html