<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/28915?offset=1640 https://bioinformaticsonline.com/opportunity/view/21894/bioinformatics-engineer-algorithm-development Wed, 01 Apr 2015 21:39:05 -0500 <![CDATA[Bioinformatics Engineer -- Algorithm Development]]> Centrillion Biosciences is a venture backed life sciences company located in Palo Alto, California. The company provides high quality genomic services to academic and industrial customers including top universities and research institutes. Centrillion Biosciences has an immediate opening for a full-time Bioinformatics Engineer. We're looking for an energetic, innovative, and motivated person who works well independently and on teams. The ideal candidate will have experience designing and implementing efficient algorithms to process large datasets. The role will involve collaborating with research scientists and other engineers, so strong communication skills are a must.

Job Description

• Work within a fast-paced, collaborative environment with small project teams working on a variety of tasks ranging from new product development to DNA data processing
• Collaborate with Centrillion research scientists in order to bridge the gap between the laboratory and the digital world
• Develop tools to enable research projects to cope with the enormous amounts of data produced by modern DNA sequencing experiments
• Build simulation algorithms to help guide and analyze research done in the lab
• Solve challenging engineering problems that require the development of innovative algorithms

Requirements

• Strong background in mathematics/statistics with a degree in a related field
• Strong analytical, coding, communication, and organizational skills
• Experience with algorithm development, simulations, and data analysis
• Proficiency in at least one modern programming language (like Python or Perl)
• Experience analyzing genetic and biological data sets (e.g., DNA data analysis and image analysis)
• Experience with machine learning and pattern recognition is preferred

Please submit your resume at https://www.centrillionbio.com/career/ to apply for this position.

]]> https://bioinformaticsonline.com/bookmarks/view/43546/introduction-to-phylogenies-in-r Wed, 13 Oct 2021 02:27:21 -0500 https://bioinformaticsonline.com/bookmarks/view/43546/introduction-to-phylogenies-in-r <![CDATA[Introduction to phylogenies in R]]> R phylogenetics is built on the contributed packages for phylogenetics in R, and there are many such packages. Let's begin today by installing a few critical packages, such as ape, phangorn, phytools, and geiger. To get the most recent CRAN version of these packages, you will need to have R 3.3.x installed on your computer!

Address of the bookmark: http://www.phytools.org/Cordoba2017/ex/2/Intro-to-phylogenies.html

]]> Abhi https://bioinformaticsonline.com/opportunity/view/22283/iihr-recruitment-2015-%E2%80%93-srf-project-asst-research-associate-posts Wed, 06 May 2015 06:13:26 -0500 <![CDATA[IIHR Recruitment 2015 – SRF, Project Asst & Research Associate Posts]]> IIHR Recruitment 2015 – SRF, Project Asst & Research Associate Posts: ICAR-Indian Institute of Horticultural Research (IIHR) has published a notification for the recruitment of Senior Research Fellow, Project Assistant and Research Associate vacancies on temporary basis. Eligible candidates may apply in prescribed application format on or before 15-05-2015. Other details like age, educational qualification, selection process, how to apply are given below…

IIHR Vacancy Details:
Total No. of Posts: 14
Name of the Post:
1. Senior Research Fellow: 12 Posts
2. Project Assistant: 01 Post
3. Research Associate: 01 Post

Age Limit: Candidates age limit is 40 years for men & 45 years for women for RA post, 35 years for men & 40 years for women for SRF post, 30 years for men & 35 years for women for JRF post and 21 to 40 years for Other as on closing date of receipt of applications. Age relaxation is applicable as per rules.

Educational Qualification: Candidates should possess M.Sc (Ag) Plant Pathology or Microbiology or Biotechnology or Biochemistry or M.Tech (Ag) or Bioinformatics for SRF Posts, 10th class with experience in workshop (welding fitting) for Project Asst Post and M.Sc (Ag) Plant Pathology or M.Sc (Ag) Biotechnology or Ph.D in Plant Pathology or Agricultural Biotechnology for RA Post.

Selection Process: Candidates will be selected based on their performance in interview.

How to Apply: Eligible candidates may send their application in the prescribed format along with attested copies of relevant certificates and should mention name of PI/ Co-PI, Item No. of the Post & name of the post clearly on the application as well as on the cover to the Concerned PI/ Co-PI, Indian Institute of Horticultural Research, Hessaraghatta Lake Post, Bengaluru-560089 on or before 15-05-2015 and attend the interview along with originals, two passport size photographs on 26 & 27-05-2015 from 10:00 AM Onwards.

Important Dates:
Last Date for Receipt of Applications: 15-05-2015.
Date & Time of Interview: 26 & 27-05-2015 from 10:00 AM Onwards.
Venue: IIHR Campus.

More at http://www.iihr.ernet.in/content/srf-jrf-application-format

]]> 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/news/view/22017/binc-2015 Sat, 11 Apr 2015 20:35:27 -0500 https://bioinformaticsonline.com/news/view/22017/binc-2015 <![CDATA[BINC 2015 !!!]]> Pondicherry University,Puducherry,on behalf of Department of Biotechnology, Government of India, will conduct the BINC examination in2015. The objective of this examination is to certify bioinformatics professionals, trained formally as well as self-trained.Registration will open from March 9,2015 to April 30,2015. Pondicherry University, Puducherry has been identified as a nodal agency by the Department of Biotechnology, Govt. of India to coordinate this examination along with nine centres namely, Pune University, Pune; Anna University, Chennai; Calcutta University, Kolkata; Institute of Bioinformatics & Applied Biotechnology, Bangalore; North-Eastern Hill University, Shillong, University of Hyderabad, Hyderabad; University of Kerala, Thiruvananthapuram; Jawaharlal Nehru University, New Delhi and Assam Agricultural University, Guwahati. In the BINC 2013 examination,17 candidates were certified. DBT has agreed to fund Research fellowships for all the BINC qualified Indian nationals to pursue Ph.D. in Indian Institutes/Universities. Note that the candidate must possess a postgraduate degree(or equivalent) & meet the criteria of the institutes/universities in order to avail research fellowship. In addition, cash prize of Rs. 10,000/- will be awarded to the top 10 BINC qualifiers.

More at http://www.binc.co.in/College/Index_New.aspx

BINC notification http://www.binc.co.in/PdfDocuments/Notification.pdf

Few dates to remember:

Starting of online submission of application: March 9, 2015
Last date for submission of application: April 30,2015
Examination consists of two parts:
Part I (Paper I) : June 7, 2015 (10 AM-12 PM)
Part II ( Paper II & III) :June 28, 2015 (9 AM-12 PM & 2 PM-4 PM)

]]> Rahul Nayak https://bioinformaticsonline.com/pages/view/35386/list-of-visualization-tools-for-network-biology Mon, 29 Jan 2018 05:12:24 -0600 https://bioinformaticsonline.com/pages/view/35386/list-of-visualization-tools-for-network-biology <![CDATA[List of visualization tools for network biology]]> Network analysis is any structured technique used to mathematically analyze a circuit (a “network” of interconnected components). The Network analysis provides the ability to quantify associations between individuals, which makes it possible to infer details about the network as a whole at the species and/or population level. Few tools published in BMC are listed here https://bmcbioinformatics.biomedcentral.com/articles/sections/networks-analysis.

image

Following are the list of standalone applications for network analysis:

Arena 3D

3D visualization of multi-layer networks

http://www.arena3d.org

Biana

Data integration and network management

http://sbi.imim.es/web/BIANA.php

BioLayout Express 3D 

2D/3D network visualization

http://www.biolayout.org/

BiologicalNetworks 

Efficient integrated multi-level analysis of microarray, sequence, regulatory and other data

http://www.biologicalnetworks.org

BioMiner

Modeling, analyzing and visualizing biochemical pathways and networks

http://www.zbi.uni-saarland.de/chair/projects/BioMiner

Cell Illustrator 

Petri nets for modeling and simulating biological networks

http://www.cellillustrator.com

COPASI

Analysis of biochemical networks and their dynamics

http://www.copasi.org/

Cytoscape 

Network visualization and analysis. Over 200 plugins [60]

http://www.cytoscape.org/

Dizzy

Chemical kinetics stochastic simulation software

http://magnet.systemsbiology.net/software/Dizzy/

DyCoNet

Gephi plugin that can be used to identify dynamic communities in networks

https://github.com/juliemkauffman/DyCoNet

GENeVis 

Network and pathway visualization

http://tinyurl.com/genevis/

GEPHI 

Interactive visualization and exploration for any network and complex system, dynamic and hierarchical graph.

https://gephi.org

Igraph

Collection of network analysis tools with the emphasis on efficiency, portability and ease of use

http://igraph.sourceforge.net

Medusa

Semantic and multi-edged simple networks

https://sites.google.com/site/medusa3visualization/

NAViGaTOR

Visualizing and analyzing protein-protein interaction networks

http://tinyurl.com/navigator1/

N-Browse

Interactive graphical browser for biological networks

http://www.gnetbrowse.org/

NeAT

Topological and clustering analysis of networks

http://rsat.ulb.ac.be/neat/

Ondex 

Data integration and visualization of large networks

http://www.ondex.org/

Osprey

Visualization and annotation of biological networks

http://biodata.mshri.on.ca/osprey/servlet/Index

Pajek 

Analysis and visualization of large networks and social network analysis

http://vlado.fmf.uni-lj.si/pub/networks/pajek/

PathwayAssist 

Navigation and analysis of biological pathways, gene regulation networks and protein interaction maps.

http://www.ariadnegenomics.com/downloads/

PIVOT 

Layout algorithms for visualizing protein interactions and families

http://acgt.cs.tau.ac.il/pivot/

ProCope 

Prediction and evaluation of protein complexes from purification data experiments

http://www.bio.ifi.lmu.de/Complexes/ProCope/

ProViz 

Visualization and exploration of interaction networks. Gene Ontology and PSI-MI formats supported

http://cbi.labri.fr/eng/proviz.htm

SpectralNET 

Network analysis and visualizations. Scatter plots and dimensionality reduction algorithms

https://www.broadinstitute.org/software/spectralnet

Tulip 

Enables the development of algorithms, visual encodings, interaction techniques, data models and domain-specific visualizations

http://tulip.labri.fr/TulipDrupal/

VANESA 

Automatic reconstruction and analysis of biological networks and Petri nets based on life-science database information

http://agbi.techfak.uni-bielefeld.de/vanesa/

VANTED 

Network reconstruction, data visualization, integration of various data types, network simulation

http://tinyurl.com/vanted/

yEd

Creation of diagrams manually and import external data

http://tinyurl.com/yEdGraph/

Web tools for network analysis

APID 

Unified protein-protein interactions from BIND, BioGRID, DIP, HPRD, IntAct and MINT

http://bioinfow.dep.usal.es/apid/

Arcadia 

Translates text-based descriptions of biological networks (SBML files) into standardized diagrams (Systems Biology Graphical Notation Process Description maps)

http://arcadiapathways.sourceforge.net/

AVIS 

Viewer for signaling networks

http://actin.pharm.mssm.edu/AVIS2

bioPIXIE 

Discovery of biological networks from diverse functional genomic data

http://pixie.princeton.edu/pixie

CellPublisher

Interactive representations of biochemical processes

http://cellpublisher.gobics.de/

Graphle

Distributed network exploration and visualization of interactive large, dense graphs

http://tinyurl.com/graphle/

GraphWeb 

Web server for graph-based analysis of biological networks

http://biit.cs.ut.ee/graphweb/

Hubba

Web-based service to explore the essential nodes in a network

http://hub.iis.sinica.edu.tw/Hubba

NetworkBLAST 

Analysis of protein interaction networks across species to infer protein complexes that are conserved in evolution

http://www.cs.tau.ac.il/~bnet/networkblast.htm

Pathview 

Tool set for pathway-based data integration and visualization

http://Pathview.r-forge.r-project.org/

PINA 

Integrated platform for protein interaction network construction, filtering, analysis, visualization and management

http://cbg.garvan.unsw.edu.au/pina/home.do

ReMatch 

Web-based tool for integration of user-given stoichiometric metabolic models into a database collected from public data sources

http://www.cs.helsinki.fi/group/sysfys/software/rematch/

SNOW 

Gene mapping on a reference or human protein-protein interaction network that SNOW hosts

http://snow.bioinfo.cipf.es

STITCH 

Resource to explore known and predicted interactions of chemicals and proteins

http://stitch.embl.de/

STRING

Protein interaction networks and integration of data such as genomic context, high-throughput experiments, conserved coexpression and previous knowledge derived from the literature

http://string-db.org

TVNViewer 

An interactive visualization tool for exploring networks that change over time or space

http://www.sailing.cs.cmu.edu/main/?page_id=545

tYNA 

System for managing, comparing and mining multiple networks

http://tyna.gersteinlab.org/tyna/

VisANT 

Visualization, mining, analysis and modeling of biological networks, metabolic networks and ecosystems

http://visant.bu.edu/

 

]]> Jit https://bioinformaticsonline.com/opportunity/view/22040/karpagam-university-coimbatore-of-sr-prof-prof-associate-and-assistant-professors-karpagam-university-coimbatore-coimbatore-tamil-nadu Thu, 16 Apr 2015 00:30:45 -0500 <![CDATA[Karpagam University, Coimbatore, of Sr. Prof, Prof, Associate and Assistant Professors Karpagam University, Coimbatore - Coimbatore, Tamil Nadu]]> Karpagam University, Coimbatore, Recruitment of Sr. Prof, Prof, Associate and Assistant Professors

Name of the College: Karpagam University, Coimbatore

Date of official publication: 15th April 2015

The newspaper wherein this job advertised: The Hindu Newspaper

Name of the posts: Senior Professors, Professors, Associate Professors and Assistant Professors

Departments:
Bioinformatics
Biotechnology
Qualifications/Eligibility: The candidates should have qualifications as M.E/M.Tech/M.A/M.Com/MBA/M.Sc/M.Phil/NET/SLET/Ph.D

Job Location: Coimbatore, TN

Salary: As per college norms

How to apply: Interested and eligible candidates are requested to apply online at http://www.karpagamuniversity.edu.in/career

Last date: As soon as possible from 15th April 2015

Reference: The Hindu Newspaper dated 15-04-2015, Coimbatore edition on 14th page

]]> https://bioinformaticsonline.com/blog/view/38238/list-of-motif-discovery-tools Tue, 20 Nov 2018 03:54:26 -0600 https://bioinformaticsonline.com/blog/view/38238/list-of-motif-discovery-tools <![CDATA[List of motif discovery tools !]]>
In genetics, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and has, or is conjectured to have, a biological significance. For proteins, a sequence motif is distinguished from a structural motif, a motif formed by the three-dimensional arrangement of amino acids which may not be adjacent.
 
Following are the list of tools for motif discovery:
 

Perform secondary structure predictions on protein sequences.

Find binding specificity information about DNA-protein complexes.

Find information about the binding specificity of DNA-binding proteins.

Use this web-based sequence motif visualization system to display sequence motif information in its appropriate three-dimensional (3D) context.

Protein function prediction and annotation in an integrated environment powered by web service.

Use to predict function from de novo protein sequences.

Search for short active protein sequences with demonstrated biological activities.

Search for ungapped segments corresponding to the most highly conserved regions of proteins.

Identify and measure surface accessible pockets as well as interior inaccessible cavities, for proteins and other molecules.

To search for catalytic residue annotation for enzymes in the Protein Data Bank.

Predict protein function using Gene Ontology.

Automatically calculate evolutionary conservation scores of key amino acid residues and map them on protein structures.

Mine the protein structure space.

Predict short linear motifs (3-8 residues) in a set of protein sequences.

A web client for visualizing protein sequence feature information using DAS.

Identify the domain architecture within a protein sequence.

Predict functional sites in eukaryotic proteins.

Use a collection of tools for protein analyses.

Predict potential protein post-translational modifications and find potential single amino acid substitutions in peptides.

Search for information related to the catalytic mechanisms of enzymes.

An integrated feature-based function prediction server for vertebrate proteomes.

Identify the closest matching PRINTS sequence motif fingerprints in a protein sequence.

Search for functional annotation of important sites in proteins with known structures.

Produce 3D conformations of small drug compounds.

A database presenting experiment-based results in human proteomics.

Conduct exhaustive intermediate profile searches of a set of homologous protein sequences.

Design protein mutations in site-directed mutagenesis.

Annotate protein using this integrated annotation resource.

Identify protein family (and DNA) domains, patterns, motifs, protein families, and functional sites.

Interactive forecasting of protein interaction hot spots.

Database containing pairs of structural analogs and their alignments.

Find sequence patterns in DNA and protein sequences.

A web server for knowledge-based modeling of protein-peptide complexes, specifically peptides in complex with major histocompatibility complex (MHC) proteins and kinases.

Find structural segments or motifs for protein structures.

Visualize protein sequence motifs on the 3D protein structures.

Find presence of any known protein motif (Prosite and Pfam) in a protein sequence.

Recognize spatial chemical binding patterns common to a set of protein structures.

Analyze proteins for the presence of N-terminal N-myristoylation site.

Find the presence of N-Glycosylation sites in human proteins.

Find the presence of O-GalNAc (mucin type) glycosylation sites in mammalian proteins.

Analyze eukaryotic proteins for the presence of serine, threonine and tyrosine phosphorylation sites.

Find possible kinase specific phosphorylation sites in eukaryotic proteins.

Predict cleavage sites at basic amino acid locations in neuropeptide precursor sequences.

Find information about patented nucleotide and protein sequences.

Search for information about glycoproteins with O-linked and C-linked glycosylation sites.

Find information about protein sequence annotations.

A server to predict protein active site residues.

Search for structural and functional information on the protein functional sites.

Search 3D protein fragments similar in structure to known active, binding and posttranslational modification sites.

Conduct genome wide functional and structural analysis.

Search for phosphorylation data of any protein of interest.

Search for information on prokaryotic proteins that undergo serine, threonine, or tyrosine phosphorylation.

Determine correct names for proteins.

Web application for predicting protein disorder by using physicochemical features and reduced amino acid set of a position-specific scoring matrix.

Find homologous protein-protein interactions across multiple species.

Search your query sequence against PROSITE pattern database for protein motifs.

Find information about protein-RNA complexes from the Protein Data Bank (PDB).

Identify protein families and domains for a given protein sequence.

A comprehensive database of pattern-recognition receptors and their ligands.

Search for short nucleotide or peptide sequences such as cis-elements in nucleotide sequences or small domains and motifs in protein sequences.

Database specialized in documenting human PPBD-containing proteins and PPBD-mediated interactions.

Predicts potential protease cleavage sites and sites cleaved by chemicals in a given protein sequence.

Predict combined transmembrane topology and signal peptides.

Search for eukaryotic phosphorylation sites.

Search for 3D structure and functional annotation of phosphorylation sites in proteins.

Search the database of in vivo phosphorylation sites of human and mouse proteins

Find information about polyglutamine (polyQ) repeats.

Find the presence of protein motifs and patterns in an amino acid sequence.

Predict signal peptide sequences and their cleavage positions in bacterial and eukaryotic amino acid sequences.

Predict protein functions based on known structures.

Predict the location of potential protein-protein binding sites for unbound proteins.

Identify short linear signatures in protein termini.

Analyze and identify newly obtained protein sequences.

Predict protein binding sites in a protein sequence based on geometrical analysis of protein tertiary substructures.

Search for evolutionarily conserved motif-like patterns in protein sequences.

Web-based server for analyzing and predicting RNA binding sites in proteins.

Search for similarities between proteins by simultaneous matching of multiple motifs.

Predict residues in protein sequences that determine the proteins' functional specificity.

Predict specificity-determining residues in protein families.

Find shared motifs in proteins with a common attribute.

Conduct in silico sumoylation sites prediction.

Search for motifs and patterns within protein sequences.

Search for motifs within proteins that are likely to be phosphorylated by specific protein kinases or bind to domains such as SH2 domains, 14-3-3 domains or PDZ domains.

Find information about populations carrying polymorphisms within protein binding pockets that make them susceptible to serious adverse drug reaction (SADR).

Search the presence of a motif in either amino acid sequence or nucleotide sequence.

Predict the presence of tyrosine sulfation sites in protein sequences

Look at protein structure from a ligand and binding site perspective.

Use a collection of bioinformatics tools at this portal site.

Find information about tandem repeats in proteins that carry fundamental biological functions and are related to a number of human diseases.

Find information about functional residues in alpha-helical and beta-barrel membrane proteins.

Database of domains and motifs with conservative location in transmembrane proteins.

Search for highly conserved and specific protein sequence motifs.

Predict functional sites in protein sequence alignments use different methodologies.

Find de novo protein motifs from chromatin immunoprecipitation data.

Scan query structures for functional sites in both proteins and nucleic acids.

Analyze quantitative structure-activity relationship of related protein families.

Search for ungapped alignments of highly conserved regions among a protein family or superfamily.

An expert system for predicting ligand-binding residues in protein structures.

Automatically identify spatially interacting motifs among distantly related proteins sharing similar folds and possessing common ancestral lineage.

]]> Neel https://bioinformaticsonline.com/file/view/22053/binc-sample-question-paper Thu, 16 Apr 2015 09:16:18 -0500 https://bioinformaticsonline.com/file/view/22053/binc-sample-question-paper <![CDATA[BINC Sample Question Paper !!!]]> BINC sample question paper. Wish you all the best for BINC examination.

]]> Jitendra Narayan https://bioinformaticsonline.com/blog/view/43260/bioinformatics-tools-for-telomere-to-telomere-assembly Tue, 17 Aug 2021 13:17:09 -0500 https://bioinformaticsonline.com/blog/view/43260/bioinformatics-tools-for-telomere-to-telomere-assembly <![CDATA[Bioinformatics tools for telomere to telomere assembly !]]> ● Merfin – k-mer-based assembly and variant calling evaluation for improved consensus accuracy (Arang Rhie)
● PanGenie – algorithm that leverages a pangenome reference built from haplotype-resolved genome assemblies in conjunction with k-mer count information from raw, short-read sequencing data to genotype a wide spectrum of genetic variation (Tobias Marschall)
● SQANTI3 – an automated pipeline for the classification of long-read transcripts that can assess the quality of data and the preprocessing pipeline (Rocío Amorín de Hegedüs @rocioadh)
● tama (Transcriptome Annotation by Modular Algorithms) – software designed for processing Iso-Seq data and other long-read transcriptome data (Richard Kuo @GenomeRIK)
● pbaa (PacBio Amplicon Analysis) – separates complex mixtures of amplicon targets from genomic samples to cluster and generate high-quality consensus sequences from HiFi reads (Zev Kronenberg @zevkronenberg)
● bellerophon – analyzes MHC typing and other low-complexity gene amplicon data; performs allele calling while detecting polymorphic sites within the sequences and removing potential chimeric sequence variants (Yuanyuan Cheng @Yuanyuan929)
● svpack – tools for filtering, comparing, and annotating structural variant (SV) calls in VCF format (Aaron Wenger)
● JumboDB – tool for de Bruijn graph construction (Anton Bankevich @AntonBankevich)
● uLTRA – tool for splice alignment of long transcriptomic reads to a genome, guided by a database of exon annotations. (Kristoffer Sahlin @krsahlin)
● LeafGo – workflow to rapidly produce high-quality de novo plant genomes (Luca Ermini @ermini_luca)

Reference:

https://www.pacb.com/blog/young-investigators-share-stellar-science-career-advice-and-bioinformatics-tools-at-smrt-leiden-2021/

 

]]> BioStar