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Center Structural Biology: Programs and Tools - http://www.csb.yale.edu
User guides and worked examples for software applications in structural and molecular biology - from Yale Univ. |
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http://www.thebiogrid.org/ - http://www.thebiogrid.org/
Database of genetic and physical interactions. It contains interaction data from many sources, including several genome/proteome-wide studies, the MIPS database, and BIND. |
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Scansite - http://scansite.mit.edu/
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. |
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SA National Bioinformatics Institute - http://www.sanbi.ac.za/
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. |
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Silva: Comprehensive Ribosomal RNA Databases - http://www.arb-silva.de
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. |
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BioModels Database - http://www.ebi.ac.uk/biomodels/
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. |
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Ligand-Gated Ion Channel Database - http://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php
LGICdb is a curated repository of genes coding for subunits of Ligand-Gated Ion Channels. |
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Bioverse - http://bioverse.compbio.washington.edu
Provides a framework for exploring the relationships among the molecular, genomic, proteomic, systems, and organismal worlds. |
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BioMolecular Engineering Research Center - http://bmerc-www.bu.edu/index.html
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. |
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Geneva Bioinformatics (GeneBio) S.A. - http://www.genebio.com/
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. |
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IBM Bioinformatics Group - Tools & Content - http://cbcsrv.watson.ibm.com/Tspd.html
Several genomics and proteomics tools, including multiple alignments, gene expression analysis, tandem repeat and motif discovery. |
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JustBio: Online Tool Set - http://www.justbio.com/tools.php
A Suite of Online tools for analysis of DNA/RNA, Proteins, and Arrays. |
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Molecular Interactions Database (MINT) - http://cbm.bio.uniroma2.it/mint/
MINT is a database designed to store functional interactions between biological molecules (proteins, RNA, DNA). |
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http://www.gene-regulation.com/ - http://www.gene-regulation.com/
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. |
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Bacterial Identification - http://pbil.univ-lyon1.fr/bibi/query.php
Service for the identification of bacteria and fungi sequences by sequence alignment. |
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http://mobyle.pasteur.fr - http://mobyle.pasteur.fr
Framework and web portal specifically designed for the integration of bioinformatics software and databanks. Provides a tutorial and an interactive guided tour. |
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http://bimas.dcrt.nih.gov/molbio/readseq/ - http://bimas.dcrt.nih.gov/molbio/readseq/
Converts amino acid and nucleotide sequence data formats including FASTA, GenBank, Phylip and others. |
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My Genomics Resource Centre - http://www.mgrc.com.my
A Malaysian Genomics toolset for high-throughput analysis of biological data. Must register to use. |
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Genepop on the Web - http://wbiomed.curtin.edu.au/genepop/
Online version of the program for populational genetics. |
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CUBIC: Columbia University Bioinformatics Center - http://cubic.bioc.columbia.edu/
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. |
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GenOuest Bioinformatics Platform - http://genouest.org
Provides a complete set of bioinformatics tools and public databanks updated daily, and a range of links to seminars, training courses and platform news. |
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Molecular Informatics Resource for the Analysis of Gene Expression - http://www.ifti.org/
Information methodologies, tools, and technologies relating to the study of gene expression and signal transduction from the Institute for Transcriptional Informatics. |
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http://mulan.dcode.org/ - http://mulan.dcode.org/
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. |
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Gene and Protein Synonyms DataBase - http://biomint.pharmadm.com
Free service for retrieving all synonyms for a given gene or protein name. |
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Canadian Bioinformatics Help Desk - http://gchelpdesk.ualberta.ca
We provide bioinformatics support, services, servers, and software to Canadian researchers. |
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DBD: Transcription Factor Prediction Database - http://dbd.mrc-lmb.cam.ac.uk
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. |
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UEA Plant sRNA Toolkit - http://srna-tools.cmp.uea.ac.uk
A suite of tools for the analysis of sRNA datasets from high-throughput sequencing experiments. |
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ProPred-I - http://www.imtech.res.in/raghava/propred1
An online service for predicting MHC binding regions in antigens. It also offers the proteasomal and immunoproteasomal filters to improve the applicability of results. |
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http://www.webact.org - http://www.webact.org
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. |
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Docking Server - http://www.dockingserver.com
Provides an internet service that calculates the site, geometry and energy of small molecules interacting with proteins. |
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YMF - DNA Motif Finding Program - http://abstract.cs.washington.edu/~saurabh/YMFWeb/YMFInput.pl
Finds novel transcription factor binding sites by searching for over-represented (most significant motifs) motifs in DNA sequences. |
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Advanced Genetics Wizard - http://www.geneticswizard.com
Online program that calculates the distribution of offspring genotypes from dominant, codominant and recessive gene crosses, for up to 6 genes. |
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LongTrace DNA Sequencing Service - https://www.nucleics.com/longtrace/
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. |
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Verbumculus Genetic Sequence Analyzer - http://www.cs.ucr.edu/~stelo/Verbumculus/
An interesting tool to discover and visualize over- or under-represented words in genetic sequences. Requires Java support in browser. Also available as a downloadable program. |
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Transterm - http://uther.otago.ac.nz/Transterm.html
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. |
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QGRS Mapper - http://bioinformatics.ramapo.edu/QGRS/
Generates information on composition and distribution of putative Quadruplex forming G-Rich Sequences (QGRS) in nucleotide sequences and NCBI genes. |
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Splice Center - http://www.tigerteamconsulting.com/SpliceCenter/SpliceOverview.jsp
Suite of user-friendly tools that evaluate the impact of gene splicing variation on specific molecular biology techniques. |
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Splice Miner - http://www.tigerteamconsulting.com/SpliceMiner/intro.jsp
Tool for querying Evidence Viewer Database (EVDB), a comprehensive, non-redundant collection of splice variant data for human genes. |
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Your Lab Data - http://www.yourlabdata.com/
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. |
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InstaSeq - http://bioinformatics.georgetown.edu/InstaSeq.htm
Google-based search engine for DNA, RNA or Protein sequences. |
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Functional Human Gene Network - http://www.genenetwork.nl
Consolidates evidence for gene-gene interactions from HPRD, BIND, Reactome, KEGG, GO, microarray co-expression and Y2H experiments. Beautiful site design. |
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PathCase: Pathways Database System - http://nashua.case.edu/pathwaysweb/
An integrated software system for storing, managing, analyzing, and querying metabolic pathways at genetic, molecular, biochemical and organism levels. |
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http://bioinfo.lifl.fr/carnac/ - http://bioinfo.lifl.fr/carnac/
A free software tool for analysing the hypothetical secondary structure of a family of homologous RNA. |
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Systems Biology of Photosynthesis - http://www.e-photosynthesis.org
Open web platform for modeling and reverse engineering of photosynthetic dynamism. |
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http://ergo.integratedgenomics.com/ERGO/ - http://ergo.integratedgenomics.com/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. |
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gp2fasta - http://gp2fasta.ovh.org/
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. |
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INCBI Irish National Centre for BioInformatics - http://acer.gen.tcd.ie/
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 |
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GenePattern - http://www.genepattern.org
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. |
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Gene Expression Data Analysis - http://bioinformatics.upmc.edu/GE2/GEDA.html
Normalization tests for differentially expressed genes, clustering, bootstrapping, leave-one-out validation, cross-fold validation. |
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Sequence Analysis (Bielefeld University Bioinformatics Server) - http://bibiserv.techfak.uni-bielefeld.de/intro/seqdept.html
Collection of sequence analysis tools. |