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 World Catalog > Science > Biology > Bioinformatics > Online Services

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World Catalog > Science > Biology > Bioinformatics > Online Services

Online Services:

Advanced Genetics Wizard

Online program that calculates the distribution of offspring genotypes from dominant, codominant and recessive gene crosses, for up to 6 genes.

http://www.geneticswizard.com

Bacterial Identification

Service for the identification of bacteria and fungi sequences by sequence alignment.

http://pbil.univ-lyon1.fr/bibi/query.php

Graand

Free Classified Ads Portal

www.graand.com

BiNCO-wiki

Provides a collection of information on data sources for biological networks, file formats that save biological networks and software to analyze the information of these sources.

http://pgrc-35.ipk-gatersleben.de/pls/htmldb_pgrc/f?p=160:1:3068865960025140

BIOBASE

The focus of the GBF project "Molecular Bioinformatics of Gene Regulation" are regulatory genomic signals and regions that govern transcriptional control based on TRANSFAC - The Transcription Factor Database. It compiles data about gene regulatory DNA sequences and protein factors binding to and acting through them.

http://www.gene-regulation.com/

BioGRID

Database of genetic and physical interactions. It contains interaction data from many sources, including several genome/proteome-wide studies, the MIPS database, and BIND.

http://www.thebiogrid.org/

BioModels Database

Resource for storing, searching and retrieving published mathematical models of biological interests. Models present in BioModels Database are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, etc.

http://www.ebi.ac.uk/biomodels/

BioMolecular Engineering Research Center

Tools and methods for computational biology. Working on secondary protein structure prediction, providing reliable profiles, and developing new ways to study molecular biology through bioinformatics.

http://bmerc-www.bu.edu/index.html

Biomolecular Interaction Network Database (BIND)

BIND is a database designed to store full descriptions of interactions, molecular complexes and pathways.

http://bind.ca

Bioverse

Provides a framework for exploring the relationships among the molecular, genomic, proteomic, systems, and organismal worlds.

http://bioverse.compbio.washington.edu

Broad Institute: Software

Scientists at the Broad Institute have developed a range of software tools for the analysis of increasingly large genome-related datasets. These are openly available to the scientific community.

http://www.broad.mit.edu/science/software/software

Canadian Bioinformatics Help Desk

We provide bioinformatics support, services, servers, and software to Canadian researchers.

http://gchelpdesk.ualberta.ca

Carnac

A free software tool for analysing the hypothetical secondary structure of a family of homologous RNA.

http://bioinfo.lifl.fr/carnac/

Center for Biological Sequence Analysis

Offers more than 30 online services for DNA and protein bioinformatics analysis.

http://www.cbs.dtu.dk/services/

Center Structural Biology: Programs and Tools

User guides and worked examples for software applications in structural and molecular biology - from Yale Univ.

http://www.csb.yale.edu

CUBIC: Columbia University Bioinformatics Center

Features PredictProtein service for sequence analysis and protein structure prediction, META for single-page interface to validated sequence analysis, PredictNLS for prediction and analysis of nuclear localization signals, EVA for evaluation of automatic protein structure prediction servers, and DSSPcont for continuous assignment of protein secondary structure.

http://cubic.bioc.columbia.edu/

DBD: Transcription Factor Prediction Database

DBD is a database of predicted transcription factors in completely sequenced genomes. The predicted transcription factors all contain assignments to sequence specific DNA-binding domain families.

http://dbd.mrc-lmb.cam.ac.uk

Docking Server

Provides an internet service that calculates the site, geometry and energy of small molecules interacting with proteins.

http://www.dockingserver.com

Entrez Browser

Retrieves molecular biology data and bibliographic citations from the NCBI's integrated databases.

http://www.ncbi.nlm.nih.gov/Entrez/

ERGO

Online service integrating biological data from genomics, biochemistry, genetics and high-throughput expression profiling, to achieve a pattern-based analysis of genes and genomes.

http://ergo.integratedgenomics.com/ERGO/

Functional Human Gene Network

Consolidates evidence for gene-gene interactions from HPRD, BIND, Reactome, KEGG, GO, microarray co-expression and Y2H experiments. Beautiful site design.

http://www.genenetwork.nl

Gene and Protein Synonyms DataBase

Free service for retrieving all synonyms for a given gene or protein name.

http://biomint.pharmadm.com

Gene Expression Data Analysis

Normalization tests for differentially expressed genes, clustering, bootstrapping, leave-one-out validation, cross-fold validation.

http://bioinformatics.upmc.edu/GE2/GEDA.html

GenePattern

This platform provides over 100 methods for the analysis and visualization of gene expression, copy number, proteomic and other data. It enables biologists to add new analyses and create workflows that can be shared, edited and published.

http://www.genepattern.org

Genepop on the Web

Online version of the program for populational genetics.

http://wbiomed.curtin.edu.au/genepop/

Geneva Bioinformatics (GeneBio) S.A.

GeneBio provides proteomics software tools and databases including SWISS-PROT, PROSITE, SWISS-2DPAGE and Melanie. We also offer a secure version of ExPASy molecular biology web server.

http://www.genebio.com/

GenOuest Bioinformatics Platform

Provides a complete set of bioinformatics tools and public databanks updated daily, and a range of links to seminars, training courses and platform news.

http://genouest.org

gp2fasta

Converts gp files from NCBI GenPept format to fasta. Its main purpose is to create fasta files with short, but still accurate headers for sequence.

http://gp2fasta.ovh.org/

IBM Bioinformatics Group - Tools & Content

Several genomics and proteomics tools, including multiple alignments, gene expression analysis, tandem repeat and motif discovery.

http://cbcsrv.watson.ibm.com/Tspd.html

iHOP

Uses the network of genes and proteins as a natural way of accessing the millions of biomedical abstracts in PubMed.

http://www.ihop-net.org/UniPub/iHOP/

INCBI Irish National Centre for BioInformatics

Hosts Irish embnet node, Gives links to Database browsing and interrogation at SRS, European (EBI) servers, Blast server for parasite genomes (EBI), US (NCBI) servers, Protein structure prediction, PredictProtein Server in Heidelberg, Gene identification, splice sites, exons, introns and a list of gene structure prediction programs

http://acer.gen.tcd.ie/

Information Génomique et Structurale (CNRS)

Online services including T-Coffee, El-Nemo, Casper and FeeBack.

http://igs-server.cnrs-mrs.fr

InstaSeq

Google-based search engine for DNA, RNA or Protein sequences.

http://bioinformatics.georgetown.edu/InstaSeq.htm

JustBio: Online Tool Set

A Suite of Online tools for analysis of DNA/RNA, Proteins, and Arrays.

http://www.justbio.com/tools.php

Ligand-Gated Ion Channel Database

LGICdb is a curated repository of genes coding for subunits of Ligand-Gated Ion Channels.

http://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php

LongTrace DNA Sequencing Service

A commercial service for improving the read length and quality of ABI 3730, 3130 and 3100 DNA sequencing traces. Works via reprocessing of the raw peak data before re-base calling. A free trial is provided.

https://www.nucleics.com/longtrace/

Mobyle

Framework and web portal specifically designed for the integration of bioinformatics software and databanks. Provides a tutorial and an interactive guided tour.

http://mobyle.pasteur.fr

Molecular Informatics Resource for the Analysis of Gene Expression

Information methodologies, tools, and technologies relating to the study of gene expression and signal transduction from the Institute for Transcriptional Informatics.

http://www.ifti.org/

Molecular Interactions Database (MINT)

MINT is a database designed to store functional interactions between biological molecules (proteins, RNA, DNA).

http://cbm.bio.uniroma2.it/mint/

Mulan

Performs single-coverage local multiple DNA sequence alignments of finished and draft-quality genome sequences. It also provides with an option to predict transcription factor binding sites evolutionarily conserved across multiple species.

http://mulan.dcode.org/

My Genomics Resource Centre

A Malaysian Genomics toolset for high-throughput analysis of biological data. Must register to use.

http://www.mgrc.com.my

NIH BioInformatics and Molecular Analysis Section

Numerous computational tools and resources to unite advances in biology with those in computers, informatics, and networking for the genomic and genetic analysis fields of BioInformatics; division of the Computational Bioscience and Engineering Lab at the Center for Information Technology.

http://bimas.dcrt.nih.gov

PANDORA

Protein ANnotation Diagram ORiented Analysis service that extracts biological information from user supplied sequences.

http://www.pandora.cs.huji.ac.il

ParAlign

Service using the ParAlign algorithm to compare genetic sequences. Apparently it is as fast as BLAST and as sensitive as Smith-Waterman.

http://www.paralign.org/

PathCase: Pathways Database System

An integrated software system for storing, managing, analyzing, and querying metabolic pathways at genetic, molecular, biochemical and organism levels.

http://nashua.case.edu/pathwaysweb/

PEDANT

Completely automatic and exhaustive analysis of protein sequence sets - from individual sequences to complete genomes

http://pedant.gsf.de/

PIR-International Protein Sequence Database

Produces a non-redundant annotated protein sequence database. PIR features integrated annotation search to support functional/structural genomics and proteomic research.

http://pir.georgetown.edu

PlasMapper

Online service to generate annotated plasmid maps up to 20 kbp. Outputs in PNG, JPG, SVG or SVGZ format.

http://wishart.biology.ualberta.ca/PlasMapper/index.html

ProPred-I

An online service for predicting MHC binding regions in antigens. It also offers the proteasomal and immunoproteasomal filters to improve the applicability of results.

http://www.imtech.res.in/raghava/propred1

ProteinLounge

Bioinformatics portal which integrates protein information and many databases and research tools useful for researchers and students. Subscription based service.

http://www.proteinlounge.com

PubCrawler

An online service for periodically performing predefined searches at NCBI, reporting new results by email or on the web.

http://pubcrawler.gen.tcd.ie/

QGRS Mapper

Generates information on composition and distribution of putative Quadruplex forming G-Rich Sequences (QGRS) in nucleotide sequences and NCBI genes.

http://bioinformatics.ramapo.edu/QGRS/

QualTrace DNA Sequencing

A free online version of the QualTrace DNA sequencing software for quality control analysis of ABI 3730 and 3730xl traces files.

http://www.nucleics.com/qualtrace-dna-sequencing-demo/index.php

ReadSeq

Converts amino acid and nucleotide sequence data formats including FASTA, GenBank, Phylip and others.

http://bimas.dcrt.nih.gov/molbio/readseq/

SA National Bioinformatics Institute

SANBI aims to bring genome information, computational biology, and analytical tools to the South African research community. Hosts SA National EMBNet Node, provides links to Sequence Retrieval System (SRS), GeneKraal, and TB Genomes Analysis Server. Research in Sequence Tag Alignment and Consensus Knowledgebase (STACK). Databases include BLAST search in Mycobacterium genome.

http://www.sanbi.ac.za/

Scansite

Scansite searches 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.

http://scansite.mit.edu/

Searching GenBank

Text and similarity searching, provided by the National Center for Biotechnology Information (NCBI).

http://www.ncbi.nlm.nih.gov/Genbank/GenbankSearch.html

Sequence Analysis (Bielefeld University Bioinformatics Server)

Collection of sequence analysis tools.

http://bibiserv.techfak.uni-bielefeld.de/intro/seqdept.html

Silva: Comprehensive Ribosomal RNA Databases

The provided databases comprise SSU and LSU sequences of all three domains. Online search and alignment tools are available and the results can be exported in ARB and FASTA format.

http://www.arb-silva.de

Simulation Programs for Teaching Population Dynamics

Offers a number of educational programs including LESLIE, LOGIST, CHAOS, CELLS, WITCOM, PRED and LEWONTIN.

http://www.dpw.wageningen-ur.nl/cwe/popeco/index.htm

Splice Center

Suite of user-friendly tools that evaluate the impact of gene splicing variation on specific molecular biology techniques.

http://www.tigerteamconsulting.com/SpliceCenter/SpliceOverview.jsp

Splice Miner

Tool for querying Evidence Viewer Database (EVDB), a comprehensive, non-redundant collection of splice variant data for human genes.

http://www.tigerteamconsulting.com/SpliceMiner/intro.jsp

Systems Biology of Photosynthesis

Open web platform for modeling and reverse engineering of photosynthetic dynamism.

http://www.e-photosynthesis.org

TFM Explorer

Scans sequences for potential Transcription Factor binding sites using Patser and TRANSFAC.

http://bioinfo.lifl.fr/TFM-Explorer/

Transterm

Interactive database of mRNA regions and motifs from all species and genomes. Users can browse the pre-computed data tables, search the sequence databases or search their own sequences.

http://uther.otago.ac.nz/Transterm.html

UEA Plant sRNA Toolkit

A suite of tools for the analysis of sRNA datasets from high-throughput sequencing experiments.

http://srna-tools.cmp.uea.ac.uk

Web Services at Institute of Microbial Technology, Chandigarh, India

Protein structure prediction (Protein Structural Classes, Secondary Structure Prediction), immunological methods (ProPred), genomics and proteomics (Genome Wise Sequence Similarity Search, Spectral Repeat Finder, 2D Gel Comparison, protein coding gene by Fast Fourier Transform), and biological databases.

http://imtech.res.in/raghava/www.html

WebACT

A database of sequence comparisons between all publicly available prokaryotic genome sequences, allowing the on-line visualisation of comparisons between up to five genomic sequences, using the Artemis Comparison Tool. User can perform their comparisons on their own data.

http://www.webact.org

YMF - DNA Motif Finding Program

Finds novel transcription factor binding sites by searching for over-represented (most significant motifs) motifs in DNA sequences.

http://abstract.cs.washington.edu/~saurabh/YMFWeb/YMFInput.pl

Your Lab Data

A free web-based Laboratory Information Management System (LIMS), aimed at a typical small molecular biology laboratory allowing members to have their own private forum, events, Electronic Lab Notebook (ELN) and a LIMS area.

http://www.yourlabdata.com/

Zinc Finger Tools

Helps users design zinc finger transcription factors.

http://www.scripps.edu/mb/barbas/zfdesign/zfdesignhome.php

US Congresswoman hangs up on Obama

A US Congresswoman hangs up the phone on President-elect Barack Obama, thinking the call is a hoax.

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Secondary school closures agreed

A council agrees to close three secondary schools and create a new Welsh medium school as part of its reorganisation plans.

news.bbc.co.uk

No decision over Shields pardon

The High Court reserves judgement in the case of jailed Liverpool fan Michael Shields, who has started a pardon bid.

news.bbc.co.uk

Controversial Lapland theme park closes down

The firm running a Lapland-style theme park in the New Forest criticised by visitors as "hell" and a "scam" close it down.

news.bbc.co.uk

Menezes family's inquest protest

The family of Jean Charles de Menezes have walked out of the inquest into his death at the Oval Cricket Ground in London in protest.

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Cash glow

How much does a street light cost for one night?

news.bbc.co.uk

Honda poised to quit Formula One

Japanese car giant Honda will withdraw from Formula One on Friday and place its team up for sale, BBC Sport understands.

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Child protection review announced

The Scottish Government announces a wide-ranging review of guidance on child protection practices.

news.bbc.co.uk

Mother guilty over Shannon kidnap

Shannon Matthews's mother and co-accused Michael Donovan are convicted of kidnapping the nine-year-old in a plot to claim a £50,000 reward.

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Nice smell...

But why else would anyone buy a new car these days?

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Carmakers 'affect entire US economy'

General Motors boss Rick Wagoner and his Ford counterpart Alan Mulally admit making mistakes in the way they ran the firms.

news.bbc.co.uk

Pompey crash out after defeat

Portsmouth exit the Uefa Cup after they lose to Bundesliga side Wolfsburg.

news.bbc.co.uk

Send your video, pictures and story ideas

Have you got a good story? BBC News wants to hear from you.

news.bbc.co.uk

DNA dilemma

Will European ruling result in more unsolved crimes?

news.bbc.co.uk

Bank cuts UK rates to 57-year low

The Bank of England has cut interest rates by one percentage point from 3% to 2%, their lowest level since 1951.

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Villa through despite Uefa Cup loss

Aston Villa fall to a shock defeat to MSK Zilina but still reach the Uefa Cup's last 32, thanks to Hamburg's victory over Slavia Prague.

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Rhys killing 'appalled country'

The murder of schoolboy Rhys Jones was a terrible killing which appalled the whole country, a judge tells a jury in his summing up.

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Canada halts parliament amid row

Canadian PM Stephen Harper secures a suspension of parliament, saving him from defeat in a confidence vote.

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Your pictures

Readers' images of snowfalls across the UK

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Kenya PM calls for Mugabe removal

Power-sharing in Zimbabwe is dead and Africa must unite to oust President Mugabe, says Kenya's prime minister.

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Smith accused of raid 'ignorance'

Jacqui Smith is attacked for not knowing a Tory MP was to be arrested, as her predecessor says she should have been told.

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Pakistan dilemma

Relations with India strained in wake of the Mumbai attacks

news.bbc.co.uk

HET will continue 'crucial work'

The special police team set up to investigate murders during the troubles is to make 75 staff redundant.

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Interest rates

Which lenders are passing on the rate cuts to customers?

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Nasa delays its next Mars mission

The US space agency (Nasa) has delayed the launch of its Mars Science Laboratory rover mission from 2009 to 2011.

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