<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/43670?offset=390 https://bioinformaticsonline.com/opportunity/view/22944/icgeb-bioinformatics-research-associate-vacancy Thu, 25 Jun 2015 20:41:00 -0500 <![CDATA[ICGEB Bioinformatics Research Associate Vacancy]]> Research Associate Position at ICGEB, New Delhi with Dr. Amit Sharma

Starting 15th July 2015, the position relates to a project specifically for in silico drug docking, screening, design, optimisation and linkage with active chemists.

Experience in many docking softwares and operating systems is essential.

Additional experience in bioinformatics and computational biology tools will be useful.

Submit curriculum vitae to: sb.icgeb@gmail.com

Closing date: 5 July 2015

]]> https://bioinformaticsonline.com/blog/view/43896/list-of-comparative-genomics-resources Tue, 28 Jun 2022 04:08:06 -0500 https://bioinformaticsonline.com/blog/view/43896/list-of-comparative-genomics-resources <![CDATA[List of comparative genomics resources !]]>

Compare structural and functional annotations of proteins between sequenced genomes.

View AREs in the human transcriptome and study the comparative genomics of AREs in model organisms.

Find information about orthologous genes in prokaryotes.

Search for publicly available QTL data on livestocks and animal species.

Find information about bovine genomics data.

A multi-organism web-based resource system designed to easily retrieve, correlate and interpret data across species.

A database resource of developmentally associated conserved non-coding elements.

Delineate conserved non-coding blocks from upstream regions of putative orthologous gene pairs from man, mouse, rat, fugu, Mus musculus, Danio rerio, and zebrafish.

Find coexpressed gene lists and networks in human and mouse.

Construct phylogenetic tree of microorganisms based on oligopeptide content of their complete proteomes.

A novel database server that classifies GenBank's dbEST (database of expressed gene sequences) libraries and removes contaminants.

Find information about the ancestral relationship between genes.

Provides an overview of the genomic organization of microRNAs and extent of conservation during evolution in different metazoan species.

Conduct comparative biometric analysis of chromosomes of different organisms.

Search for Indices of gene and transcripts in human and mouse.

Search and compare 12 new and old Drosophila genomes.

Access to whole genome alignments of human, mouse, rat and fish sequences.

Find eukaryotic paralog/paralogon information.

Analyze the evolutionary process of overlapping genes when comparing different species.

The first publicly available system reported to handle inter-species gene mention normalization.

A web-based software/database system aimed at an improved and accelerated annotation of prokaryotic genomes.

Visualize gene indices of human, mouse, Arabidopsis, Zebrafish, Drosophila and Sheep.

Find information about mutated mouse genes.

A data management and analysis system for metagenomes

Search for influenza sequence, vaccine, and drug resistance information.

LAMHDI, the initiative to Link Animal Models to Human DIsease, is designed to accelerate the research process by providing biomedical researchers with a simple, comprehensive Web-based resource to find the best animal models for their research.

The missing link between multi-species full genome comparisons and functional analysis.

Conduct comparative analysis of completely sequenced microbial genomes.

A biologist-centric software for evolutionary analysis of DNA and protein sequences.

Conduct single nucleotide polymorphisms diversity measurements among homologous sequences from the Mammalia class.

Find information about 1000s of microbial genomes.

A database dedicated to the study of genome conservation.

Explore orthologous relations across 352 complete genomes.

Browse complete genomes in several clades.

A database of orthologous genomic markers for placental mammal phylogenetics.

Conduct genome wide functional and structural analysis.

Conduct genome-wide cis-regulatory module (CRM) predictions for both the human and the mouse genomes.

Compare phenotypes of a given gene or gene set in different model organisms.

Phylemon is a web server that integrates a selected suite of more than 20 different tools from the most popular stand-alone programs of phylogenetic and evolutionary analysis.

Use this database to see where in the evolution some phylogenetic lineages were started, and over which species they were contained.

Search for genomic information on nematode satellite species Pristionchus pacificus.

Find information about related protein sequences.

Database hosting genomics and post-genomics data from multiple protozoans.

A database of pseudogene families based on the protein families from the Pfam database.

Find genomic information about mammals.

Find information about predicted regulons in prokaryotic transcription regulation.

Perform systematic comparison of proteome data among species.

A comparative map viewer dedicated to the biology of the Solanaceae family.

Analyze data from functional analysis on fragmented microbial genetic material.

Visualize and explore comparative genomic hybridization data sets.

Search for genome-wide annotations of regulatory sites in yeast and prokaryotes genomes.

Search for information on adaptive evolution in gene families of higher plants and chordate.

Generate graphical maps of circular genomes that show sequence features, base composition plots, analysis results and sequence similarity plots.

Conduct a comprehensive analysis of genes and genomes.

An interactive online poster presentation on the Macaque genome, including high-quality images, video clips, and Web resources

Search for annotated genetic information of expressed sequence tags (ESTs) in different eukaryotic organisms.

Find mapping and expression information for a unigene cluster (ESTs and full-length mRNA sequences organized into clusters that each represent a unique known or putative gene)

A public online resource for identifying or designing 'universal' overgo-hybridization probes from conserved sequences that can be used to efficiently screen one or more genomic libraries from a designated group of species.

Comprehensive suite of programs and databases for comparative analysis of genomic sequences.

Find metabolic networks and phylogenomic information on a taxonomically diverse range of eukaryotes.

]]> Shruti Paniwala https://bioinformaticsonline.com/opportunity/view/23384/research-scientist-at-dupont Fri, 17 Jul 2015 20:36:17 -0500 <![CDATA[Research Scientist at DuPONT]]> Research Scientist
Hyderabad, Telangana
Job Description

Job Description

The Global Trait Discovery Informatics (GTDI) group located at the DuPont Knowledge Centre (DKC), Hyderabad, India is currently seeking applications for a highly motivated computational biologist. The GTDI group contributes to research programs in plant biotechnology at the DKC as well as across research centers located in DuPont Pioneer, Johnston, Iowa and at the DuPont Experimental Station in Wilmington, Delaware.

We are looking for candidates who have experience in analysis of high-throughput -omics datasets. The researcher will be primarily responsible for analyzing diverse -omics datatypes, such as transcriptomics, proteomics and metabolomics and actively contribute towards building streamlined solutions.

The candidate will be part of a diverse team of experimental biologists, computational biologists and software developers. A critical aspect of this position involves working with global teams across multiple locations and will require effective project coordination and communication skills. This is an exciting opportunity for candidates with strong data driven skills, who want to work at the interface of computational and experimental biology and contribute towards scientific discovery.

Responsibilities

·Integrate and analyze multiple datatypes in the context of experimental observations with a goal towards formulating testable hypothesis.

·Understanding the research questions from experimental biologists and formulate relevant in silico analyses.

·Establish and implement systematic analysis workflows starting from processing of raw data to biological interpretation.

·Critically analyze a wide variety of experimental data with a view to solving the underlying research questions.

·Identify and generate datasets for scientific testing and evaluation of algorithms.

Qualifications

PhD in computational biology, bioinformatics, population genetics, complex systems, computer sciences or any relevant physical or mathematical sciences, with experience in analyzing diverse -omics datasets.

Job Qualifications

Qualifications

PhD in computational biology, bioinformatics, population genetics, complex systems, computer sciences or any relevant physical or mathematical sciences, with experience in analyzing diverse -omics datasets.

More at http://careers.dupont.com/jobsearch/job-details/research-scientist/006077W-01/

]]> https://bioinformaticsonline.com/blog/view/44401/bioinformatics-tools-for-phylogeny Mon, 06 Nov 2023 03:09:59 -0600 https://bioinformaticsonline.com/blog/view/44401/bioinformatics-tools-for-phylogeny <![CDATA[Bioinformatics Tools for Phylogeny !]]> Direct access to the individual tools available on this server.

Multiple Alignment:Phylogeny:Tree viewers:Utilities:
MUSCLE PhyML TreeDyn Gblocks
T-Coffee / 3DCoffee TNT Drawgram Jalview
ClustalW BioNJ Drawtree Readseq
ProbCons MrBayes ATV (A Tree Viewer) Built-in converter
]]> BioStar https://bioinformaticsonline.com/opportunity/view/23247/ra-at-csir-urdip Fri, 10 Jul 2015 18:34:03 -0500 <![CDATA[RA at CSIR-URDIP]]> CSIR - UNIT FOR RESEARCH AND DEVELOPMENT OF INFORMATION PRODUCTS (CSIR- URDIP)

Adv. No. URDIP/ 15/2015

Opportunity for young Bioinformatics Professionals to make a career in the area of Intellectual Property

CSIR has set up a Unit for Research and Development of Information Products (CSIRURDIP) at Pune to work in the area of scientific informatics. One of the major focus areas of research work at CSIR-URDIP is PATENT INFORMATICS. With the increasing applications of Bioinformatics in the areas of life sciences industry such as Agriculture and Health Care (Diagnostics and Drugs), the output of research in these area is being protected by different forms of Intellectual Property rights. Realizing the importance of IP in the Bioinformatics field, Department of Biotechnology (DBT) has sanctioned a project on “Development, Facilitation and Harvesting of Bioinformatics related Intellectual Property” at CSIR-URDIP.

The project will involve application of Patent Informatics tools and techniques to Bioinformatics (including creation of patent landscapes, preparation of techno-legal reports of patentability, freedom to operate studies) to help protect IPRs and develop and conduct training programmes on IPRs related to Bioinformatics.

CSIR-URDIP invites applications from young Bioinformatics professionals to work on this emerging area which offers challenging opportunities and attractive career possibilities in future.

Position I: Research Associate

No of Positions: One

Consolidated amount Payable: = Rs 26,400.00

Qualification: PhD in Bioinformatics. In exceptional cases, candidature of M. Tech. candidates with First class in Bioinformatics with three years of relevant work experience will also be considered.

Job requirement: The prospective candidate will be expected to identify patents/scientific literature in field of Bioinformatics, evaluate them Vis a Vis other patents in fields and come up landscape / FTO / Patentability reports.

Age Limit: 35 years.

The candidates meeting the above criteria may appear for walk in interview at their cost on Monday 13th July 2015 at 02:00 p.m. with the CV and supporting documents (original plus copies) at the following address: CSIR Unit or Research and Development of Information Products (URDIP), "Tapovan" S.No. 113 & 114, Near NCL Colony Baner Side Gate, NCL Estate, Pashan Road, Pune-411008, Maharashtra, India

Advertisement: www.urdip.res.in/download/DBT_RA_Advt_July%202015.pdf

]]> https://bioinformaticsonline.com/pages/view/34221/alignment-free-sequence-comparison-tools-available-for-next-generation-sequencing-data-analysis Tue, 07 Nov 2017 05:33:33 -0600 https://bioinformaticsonline.com/pages/view/34221/alignment-free-sequence-comparison-tools-available-for-next-generation-sequencing-data-analysis <![CDATA[Alignment-free sequence comparison tools available for next-generation sequencing data analysis]]>

kallisto

Transcript abundance quantification from RNA-seq data (uses pseudoalignment for rapid determination of read compatibility with targets)

Software (C++)

https://pachterlab.github.io/kallisto/

Sailfish

Estimation of isoform abundances from reference sequences and RNA-seq data (k-mer based)

Software (C++)

http://www.cs.cmu.edu/~ckingsf/software/sailfish/

Salmon

Quantification of the expression of transcripts using RNA-seq data (uses k-mers)

https://combine-lab.github.io/salmon/

RNA-Skim

RNA-seq quantification at transcript-level (partitions the transcriptome into disjoint transcript clusters; uses sig-mers, a special type of k-mers)

Software (C++)

http://www.csbio.unc.edu/rs/

Variant calling

ChimeRScope

Fusion transcript prediction using gene k-mers profiles of the RNA-seq paired-end reads

Software (Java)

https://github.com/ChimeRScope/ChimeRScope/wiki

FastGT

Genotyping of known SNV/SNP variants directly from raw NGS sequence reads by counting unique k-mers

Software (C)

https://github.com/bioinfo-ut/GenomeTester4/

Phy-Mer

Reference-independent mitochondrial haplogroup classifier from NGS data (k-mer based)

Software (Python)

https://github.com/danielnavarrogomez/phy-mer

LAVA

Genotyping of known SNPs (dbSNP and Affymetrix's Genome-Wide Human SNP Array) from raw NGS reads (k-mer based)

Software (C)

http://lava.csail.mit.edu/

MICADo

Detection of mutations in targeted third-generation NGS data (can distinguish patients’ specific mutations; algorithm uses k-mers and is based on colored de Bruijn graphs)

Software (Python)

http://github.com/cbib/MICADo

General mapper

Minimap

Lightweight and fast read mapper and read overlap detector (uses the concept of “minimazers”, a special type of k-mers)

Software (C)

https://github.com/lh3/minimap

Assembly

De novo genome assembly

MHAP

Produces highly continuous assembly (fully resolved chromosome arms) from third-generation long and noisy reads (10 kbp) using a dimensionality reduction technique MinHash

Software (Java)

https://github.com/marbl/MHAP

Miniasm

Assembler of long noisy reads (SMRT, ONT) using the Overlap-Layout Consensus (OLC) approach without the necessity of an error correction stage (uses minimap)

Software (C)

https://github.com/lh3/miniasm

LINKS

Scaffolding genome assembly with error-containing long sequence (e.g., ONT or PacBio reads, draft genomes)

Software (Perl)

https://github.com/warrenlr/LINKS/

Read clustering

afcluster

Clustering of reads from different genes and different species based on k-mer counts

Software (C++)

https://github.com/luscinius/afcluster

QCluster

Clustering of reads with alignment-free measures (k-mer based) and quality values

Software (C++)

http://www.dei.unipd.it/~ciompin/main/qcluster.html

Reads error correction

Lighter

Correction of sequencing errors in raw, whole genome sequencing reads (k-mer based)

Software (C++)

https://github.com/mourisl/Lighter

QuorUM

Error corrector for Illumina reads using k-mers

Software (C++)

https://github.com/gmarcais/Quorum

Trowel

Software (C++)

https://sourceforge.net/projects/trowel-ec/

Metagenomics

Assembly-free phylogenomics

AAF

Phylogeny reconstruction directly from unassembled raw sequence data from whole genome sequencing projects; provides bootstrap support to assess uncertainty in the tree topology (k-mer based)

Software (Python)

https://github.com/fanhuan/AAF

kSNP v3

Reference-free SNP identification and estimation of phylogenetic trees using SNPs (based on k-mer analysis)

Software (C)

https://sourceforge.net/projects/ksnp/files/

NGS-MC

Phylogeny of species based on NGS reads using alignment-free sequence dissimilarity measures d2* and d2 S under different Markov chain models (using k-words)

R package

http://www-rcf.usc.edu/~fsun/Programs/NGS-MC/NGS-MC.html

Species identification/taxonomic profiling

CLARK

Taxonomic classification of metagenomic reads to known bacterial genomes using k-mer search and LCA assignment

Software (C++)

http://clark.cs.ucr.edu/

FOCUS

Reports organisms present in metagenomic samples and profiles their abundances (uses composition-based approach and non-negative least squares for prediction)

Web service Software (Python)

http://edwards.sdsu.edu/FOCUS/

GSM

Estimation of abundances of microbial genomes in metagenomic samples (k-mer based)

Software (Go)

https://github.com/pdtrang/GSM

Mash

Species identification using assembled or unassembled Illumina, PacBio, and ONT data (based on MinHash dimensionality-reduction technique)

Software (C++)

https://github.com/marbl/mash

Kraken

Taxonomic assignment in metagenome analysis by exact k-mer search; LCA assignment of short reads based on a comprehensive sequence database

Software (C++)

https://ccb.jhu.edu/software/kraken/

LMAT

Assignment of taxonomic labels to reads by k-mers searches in precomputed database

Software (C++/Python)

https://sourceforge.net/projects/lmat/

stringMLST

k-mer-based tool for MLST directly from the genome sequencing reads

Software (Python)

http://jordan.biology.gatech.edu/page/software/stringMLST

Taxonomer

k-mer-based ultrafast metagenomics tool for assigning taxonomy to sequencing reads from clinical and environmental samples

Web service

http://taxonomer.iobio.io/

Other

d2-tools

Word-based (k-tuple) comparison (pairwise dissimilarity matrix using d2S measure) of metatranscriptomic samples from NGS reads

Software (Python/R)

https://code.google.com/p/d2-tools/

VirHostMatcher

Prediction of hosts from metagenomic viral sequences based on ONF using various distance measures (e.g., d2)

Software (C++)

https://github.com/jessieren/VirHostMatcher

MetaFast

Statistics calculation of metagenome sequences and the distances between them based on assembly using de Bruijn graphs and Bray–Curtis dissimilarity measure

Software (Java)

https://github.com/ctlab/metafast

]]> Abhimanyu Singh https://bioinformaticsonline.com/opportunity/view/23277/project-fellow-at-ihbt-palampur-himachal-pradesh Sun, 12 Jul 2015 07:54:37 -0500 <![CDATA[Project Fellow at IHBT - Palampur, Himachal Pradesh]]> The Institute is working relentlessly on developing technologies for sustainable utilization of Himalayan bioresources, and in the area of tea, floriculture, bamboos and medicinal and aromatic plants. Looking at the mission of the Institute,the quantum of work undertaken and milestones achieved it was rightly conceived to rename the Institute from CSIR Complex Palampur to Institute of Himalayan Bioresource Technology at a high level meeting. Finally the Institute received its new name Institute of Himalayan Bioresource Technology (IHBT) in 1997 by then Prime Minister Shri H.D. Deve Gowda. Till date this is the only kind of National R&D laboratory in the state of Himachal.

Detail Of Institute of Himalayan Bioresource Technology (IHBT) Project Fellow Recruitment:

No.of Posts: 02

Qualification : 1st Class B. Tech. in Bioinformatics/ Computational Biology Or M.Sc. in Bioinformatics/ Computational Biology with 55% marks OR M.Tech. in Bioinformatics/ Computational Biology with 55% marks.

Age : 28 years as on 10.06.2015

Pay Scale: Rs.12,000/- P.M/Rs.14,000/- P.M.

Age : 35 years,(Up to 40 years for members of SC/STs).

Selection Procedure For Institute of Himalayan Bioresource Technology (IHBT) – Project Fellow Post:

Written Test on 10/06/2015.

Shortlisted candidates will undertake face to face interview.

Dates are yet to be announced for the final selection

Walkin Procedure For Project Fellow vacancy in Institute of Himalayan Bioresource Technology (IHBT):

Eligible candidates may appear for Walk-in-Interview on Date : 10.06.2015, Time 9:00 A.M. Venue : CSIR- IHBT Palampur (H.P.) alongwith an application on prescribed format. Candidates must also bring with them original certificates of testimonials at the time of the appearing for interview failing which he/she will not be allowed to appear for interview.

Important Dates To Remember :
Walk in date for this job : 10/06/2015

]]> https://bioinformaticsonline.com/bookmarks/view/36512/hisat2-a-fast-and-sensitive-alignment-program-for-mapping-next-generation-sequencing-reads Tue, 08 May 2018 04:27:22 -0500 https://bioinformaticsonline.com/bookmarks/view/36512/hisat2-a-fast-and-sensitive-alignment-program-for-mapping-next-generation-sequencing-reads <![CDATA[HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads]]> 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

]]> Rahul Nayak https://bioinformaticsonline.com/opportunity/view/23369/assistant-professor-professor-at-central-university-of-south-bihar Thu, 16 Jul 2015 22:36:53 -0500 <![CDATA[Assistant Professor/ Professor at Central University of South Bihar]]> Central University of South Bihar

(Established under Central Universities Act, 2009)

BIT Campus, PO: B.V. College,

Patna – 800 014 (Bihar)

Employment Notice No. CUSB / 27 / Faculty / 2015

Appointment for Faculty Positions Applications in the prescribed form are invited from the eligible candidates for the following posts shown against the subjects to be filled up on regular/contract/re-employment after superannuation basis:

1 Bioinformatics - 03 Posts

2 Biotechnology – 02 Posts

12 Life Science – 04 Posts

The duly filled in application form, complete in all respect along with fee must be sent only by Speed post/Registered post/Courier to The Registrar, Central University of South Bihar, BIT Campus, P.O. : B.V. College, Patna-800014.

Last Date of Receiving Application 10th August, 2015

Advertisement:

http://cub.ac.in/index.php?option=com_content&view=article&id=31&Itemid=157

]]> https://bioinformaticsonline.com/bookmarks/view/37915/dna-nucleotide-counter Fri, 12 Oct 2018 04:37:01 -0500 https://bioinformaticsonline.com/bookmarks/view/37915/dna-nucleotide-counter <![CDATA[DNA Nucleotide Counter]]> DNA Nucleotide Counter is delivered in a DNA Baser package together with other free molecular biology tools. Download the package and double click it. The programs inside the package will be extracted to the destination folder (specified by you). Go to the destination folder and double click the program you want to use.

It installs in any computer even if you don't have administrator rights!

Address of the bookmark: http://www.dnabaser.com/download/DNA-Counter/index.html

]]> Neel