BOL: Related items

The Kingsley Lab

Fri, 03 Jun 2016 09:55:10 -0500

The Molecular Basis of Vertebrate Evolution. Naturally occurring species show spectacular differences in morphology, physiology, behavior, disease susceptibility, and life span. Although the genomes of many organisms have now been completely sequenced, Kingsley lab still know relatively little about the specific DNA sequence changes that underlie interesting species-specific traits. Kingsley lab laboratory is using a combination of genetic and genomic approaches to identify the detailed molecular mechanisms that control evolutionary change in vertebrates.

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

NearHGT

Jit — Wed, 22 Jun 2016 05:41:57 -0500

Horizontal gene transfer (HGT), the transfer of genetic material between organisms, is crucial for genetic innovation and the evolution of genome architecture. Existing HGT detection algorithms rely on a strong phylogenetic signal distinguishing the transferred sequence from ancestral (vertically derived) genes in its recipient genome. Detecting HGT between closely related species or strains is challenging, as the phylogenetic signal is usually weak and the nucleotide composition is normally nearly identical. Nevertheless, there is a great importance in detecting HGT between congeneric species or strains, especially in clinical microbiology, where understanding the emergence of new virulent and drug-resistant strains is crucial, and often time-sensitive.

We developed a novel, self-contained technique named Near HGT, based on the synteny index, to measure the divergence of a gene from its native genomic environment and used it to identify candidate HGT events between closely related strains. The method confirms candidate transferred genes based on the constant relative mutability (CRM). Using CRM, the algorithm assigns a confidence score based on “unusual” sequence divergence. A gene exhibiting exceptional deviations according to both synteny and mutability criteria, is considered a validated HGT product. We first employed the technique to a set of three E. coli strains and detected several highly probable horizontally acquired genes. We then compared the method to existing HGT detection tools using a larger strain data set.

When combined with additional approaches our new algorithm provides richer picture and brings us closer to the goal of detecting all newly acquired genes in a particular strain.

Availability: The method is publicly available athttp://research.haifa.ac.il/~ssagi/software/nearHGT.zip

Address of the bookmark: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004408

Kaiju

Jit — Mon, 27 Jun 2016 11:23:04 -0500

Kaiju is a program for the taxonomic classification of metagenomic high-throughput sequencing reads. Each read is directly assigned to a taxon within the NCBI taxonomy by comparing it to a reference database containing microbial and viral protein sequences.

By default, Kaiju uses either the available complete genomes from NCBI RefSeq or the microbial subset of the non-redundant protein database nr used by NCBI BLAST, optionally also including fungi and microbial eukaryotes.

Kaiju translates reads into amino acid sequences, which are then searched in the database using a modified backward search on a memory-efficient implementation of the Burrows-Wheeler transform, which finds maximum exact matches (MEMs), optionally allowing mismatches in the protein alignment. The search can process up to millions of reads per minute using, for example, only 10 GB RAM with a protein database comprising 4821 microbial genomes. Kaiju can also be used for querying any other protein database without taxonomic classification, using either protein or nucleotide queries.

Kaiju is described in Menzel, P. et al. (2016) Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nat. Commun. 7:11257 (open access).

Address of the bookmark: http://kaiju.binf.ku.dk/

Advertisement for Junior Research Fellow(JRF) at School of Computational and Integrative Sciences Jawaharlal Nehru University

Thu, 14 Jul 2016 07:24:53 -0500

Advertisement for Junior Research Fellow(JRF) - (1)

Applications are invited for a post in DST, India funded Project entitled: "Positive and negative impacts of macromolecular crowding agents during target site location by DNA binding proteins – origin of optimal search at physiological ionic concentration (Reference Number: ECR/2016/000188) ''. The selected candidate will be appointed purely on temporary basis, initially for two years as a JRF that may be extended to one year of SRF based on the performance.

Position: Junior Research Fellow (1)

Qualifications & Experience: Candidate must have a consistently good academic record with at least 60% marks in all throughout and must have qualified NET/GATE.

Desirable: Basic knowledge in the field of biophysics, molecular simulations and computational biology are desirable.

Salary: Consolidated Rs. 25,000 per month.

Tenure: The project duration is for three years and the selected candidate would be appointed after an interview. Appointment will be purely on temporary basis as stipulated by the existing rules of the University.

Interested candidates need to send an application to the address mentioned below mentioning the name of the project and post applied for (on the cover of the envelope).

The applications along with CV should be mailed at the address given below. Name, address, contact number and e. mail address of two referees must be enclosed with the application. The last date for the application is July 31st 2016.

Dr. Arnab Bhattacharjee (Principal Investigator)
Assistant Professor
School of Computational and Integrative Sciences
Jawaharlal Nehru University
New Delhi-110067
E-mail: arnab@jnu.ac.in

Note: 1. Only shortlisted candidates will be communicated to appear in the interview at SCIS, JNU and no other communications in this regard will be entertained.

2. No TA/DA will be paid for appearing in interview.

Synteny Portal: a web-based application portal for synteny block analysis

Jit — Wed, 24 May 2017 10:39:23 -0500

Synteny Portal, a versatile web-based application portal for constructing, visualizing and browsing synteny blocks. With Synteny Portal, users can easily (i) construct synteny blocks among multiple species by using prebuilt alignments in the UCSC genome browser database, (ii) visualize and download syntenic relationships as high-quality images, (iii) browse synteny blocks with genetic information and (iv) download the details of synteny blocks to be used as input for downstream synteny-based analyses, all in an intuitive and easy-to-use web-based interface. We believe that Synteny Portal will serve as a highly valuable tool that will enable biologists to easily perform comparative genomics studies by compensating limitations of existing tools. Synteny Portal is freely available at http://bioinfo.konkuk.ac.kr/synteny_portal.

http://bioinfo.konkuk.ac.kr/synteny_portal/

Address of the bookmark: http://bioinfo.konkuk.ac.kr/synteny_portal/

JRF Bioinformatics at IIT, Delhi

Mon, 25 Jul 2016 03:26:20 -0500

No. IITD/IRD/RP03017/4254/Advertisement No.: IITD/IRD/093/2016
JRF Bioinformatics job vacancies in Indian Institute of Technology Delhi (IIT Delhi)
Title : Elucidation of Pathologically Relevant miRNAs Responsible for Disease Progression and Resistance to Chemotherapy in Chronic Lymphocytic Leukemia (CLL) (RP03017)
Qualification : Candidates having first class B. Tech. / M.Sc. Degree or equivalent in Bioinformatics or Biotechnology with NET qualification. Desirable: Candidates having computer programming skills (C++, Python, Java, Web designing using Materialize frameworks, database management, offline software GUI development) with knowledge of Linux server environment and / or experience in next generation sequencing (NGS) data analysis, MD simulations will be preferred.
No. of Post : 01
Pay Scale : Rs.25,000/-
How to apply
Walk-in test / interview will be held on 04/08/2016, 03.00 p.m. at Committee Room No. 230, Block-I, Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi-110016.

More at http://ird.iitd.ac.in/sites/default/files/jobs/project/IITD-IRD-093-2016.pdf

SOAP2 : Short Oligonucleotide Analysis Package 2

Poonam Mahapatra — Wed, 23 May 2018 10:09:22 -0500

SOAPaligner/soap2 is a member of the SOAP (Short Oligonucleotide Analysis Package). It is an updated version of SOAP software for short oligonucleotide alignment. The new program features in super fast and accurate alignment for huge amounts of short reads generated by Illumina/Solexa Genome Analyzer. Compared to soap v1, it is one order of magnitude faster. It require only 2 minutes aligning one million single-end reads onto the human reference genome. Another remarkable improvement of SOAPaligner is that it now supports a wide range of the read length. SOAPaligner benefitted in time and space efficiency by a revolution in the basic data structures and algorithms used.The core algorithms and the indexing data structures (2way-BWT) are developed by the algorithms research group of the Department of Computer Science, the University of Hong Kong (T.W. Lam, Alan Tam, Simon Wong, Edward Wu and S.M. Yiu).

Address of the bookmark: http://soap.genomics.org.cn/soapaligner.html

Research Associate (Computer Sciences) recruitment in National Bureau of Plant Genetic Resources

Thu, 28 Jul 2016 04:39:13 -0500

Research Associate (Computer Sciences) recruitment in National Bureau of Plant Genetic Resources

Project: Indo-UK Centre for improvement of Nitrogen use efficiency in wheat Dr. Soma S. Marla, Pr. Scientist (Bioinformatics), Division of Genomic Resources, ICAR, NBPGR, ND.

Qualification: Ph.D. Degree in Computer Sciences/Bioinformatics OR 1. First class Master’s degree in any discipline of Plant Sciences with specialization in Computer Sciences/ Bioinformatics having 1st division or 60% marks or equivalent overall grade point average with at least two years of research experience as evidenced from Fellowship/ Associate ship. 2. NET qualification is essential for the candidates with 3+2 years B.Sc.+ M.Sc. Desirable: Demonstrated experience & skills in database design, management, UNIX OS, in NGS data analysis. Experience substantiated by publications of high quality will be preferred.

No.of Post: 1

Pay Scale: Rs. 40,000 (Ph.D)/ Rs + 30 % HRA; Rs.38,000 ( Masters Degree 0 + 30 % HRA).

Age Limit : below 40 years for RA position
How to apply
Applicants for RA post should send their complete CV (Advance copy of the application may be sent by email to :soma.marla@icar.gov.in or ssmarl@yahoo.com, should enclose the copy of the research publications; one page summary of their achievement relevant to the post applied for; and should enclose two reference letters (one must be from the person with whom worked latest). Shortlisted candidate will be intimated for interview by email.

The candidates who wish to attend the walk-in interview are requested to bring with them five copies of the CV (one copy with photograph) as per the format given below. Also, the candidates should bring the original documents such as degree certificates, marks sheets, publications, thesis, experience certificate etc. for verification.

Date of Interview: 17.8.2016.

More at http://www.nbpgr.ernet.in/Downloadfile.aspx?EntryId=7133

S-plot2: Rapid Visual and Statistical Analysis of Genomic Sequences

Abhimanyu Singh — Tue, 02 Oct 2018 17:57:27 -0500

S-plot2 creates an interactive, two-dimensional heatmap capturing the similarities and dissimilarities in nucleotide usage between genomic sequences (partial or complete). In S-plot2, whole eukaryotic chromosomes and smaller prokaryotic genomes can be efficiently compared. The tool includes functionality to extract, analyze, and automate BLAST queries of regions of interest within the heatmap. This facilitates the investigation of quickly evolving coding regions, novel coding regions, and laterally transferred elements.

Address of the bookmark: https://bitbucket.org/lkalesinskas/splot