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Directories (14)
Ecological Databases (1)
Gene Expression and Regulation (10)

Genome Databases (19)
Homology Detection (14)
Molecular Biology Tools (10)

Phylogenetic Analysis (10)
Protein Analysis (45)
Software (107)

Web Pages

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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.

Bacterial Identification - http://pbil.univ-lyon1.fr/bibi/query.php
Service for the identification of bacteria and fungi sequences by sequence alignment.

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

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.

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.

Biomolecular Interaction Network Database (BIND) - http://bind.ca
BIND is a database designed to store full descriptions of interactions, molecular complexes and pathways.

Bioverse - http://bioverse.compbio.washington.edu
Provides a framework for exploring the relationships among the molecular, genomic, proteomic, systems, and organismal worlds.

Broad Institute: Software - http://www.broad.mit.edu/science/software/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.

Canadian Bioinformatics Help Desk - http://gchelpdesk.ualberta.ca
We provide bioinformatics support, services, servers, and software to Canadian researchers.

Center for Biological Sequence Analysis - http://www.cbs.dtu.dk/services/
Offers more than 30 online services for DNA and protein bioinformatics analysis.

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.

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.

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.

Docking Server - http://www.dockingserver.com
Provides an internet service that calculates the site, geometry and energy of small molecules interacting with proteins.

Entrez Browser - http://www.ncbi.nlm.nih.gov/Entrez/
Retrieves molecular biology data and bibliographic citations from the NCBI's integrated databases.

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.

Gene and Protein Synonyms DataBase - http://biomint.pharmadm.com
Free service for retrieving all synonyms for a given gene or protein name.

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.

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.

Genepop on the Web - http://wbiomed.curtin.edu.au/genepop/
Online version of the program for populational genetics.

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.

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.

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.

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.

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.

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.

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.

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.

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.

http://www.ihop-net.org/UniPub/iHOP/ - http://www.ihop-net.org/UniPub/iHOP/
Uses the network of genes and proteins as a natural way of accessing the millions of biomedical abstracts in PubMed.

http://www.pandora.cs.huji.ac.il - http://www.pandora.cs.huji.ac.il
Protein ANnotation Diagram ORiented Analysis service that extracts biological information from user supplied sequences.

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.

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.

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.

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

Information Génomique et Structurale (CNRS) - http://igs-server.cnrs-mrs.fr
Online services including T-Coffee, El-Nemo, Casper and FeeBack.

InstaSeq - http://bioinformatics.georgetown.edu/InstaSeq.htm
Google-based search engine for DNA, RNA or Protein sequences.

JustBio: Online Tool Set - http://www.justbio.com/tools.php
A Suite of Online tools for analysis of DNA/RNA, Proteins, and Arrays.

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.

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.

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.

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).

My Genomics Resource Centre - http://www.mgrc.com.my
A Malaysian Genomics toolset for high-throughput analysis of biological data. Must register to use.

NIH BioInformatics and Molecular Analysis Section - http://bimas.dcrt.nih.gov
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.

ParAlign - http://www.paralign.org/
Service using the ParAlign algorithm to compare genetic sequences. Apparently it is as fast as BLAST and as sensitive as Smith-Waterman.

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.

PIR-International Protein Sequence Database - http://pir.georgetown.edu
Produces a non-redundant annotated protein sequence database. PIR features integrated annotation search to support functional/structural genomics and proteomic research.

PlasMapper - http://wishart.biology.ualberta.ca/PlasMapper/index.html
Online service to generate annotated plasmid maps up to 20 kbp. Outputs in PNG, JPG, SVG or SVGZ format.

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.

ProteinLounge - http://www.proteinlounge.com
Bioinformatics portal which integrates protein information and many databases and research tools useful for researchers and students. Subscription based service.

PubCrawler - http://pubcrawler.gen.tcd.ie/
An online service for periodically performing predefined searches at NCBI, reporting new results by email or on the web.

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.

QualTrace DNA Sequencing - http://www.nucleics.com/qualtrace-dna-sequencing-demo/index.php
A free online version of the QualTrace DNA sequencing software for quality control analysis of ABI 3730 and 3730xl traces files.

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.

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.

Searching GenBank - http://www.ncbi.nlm.nih.gov/Genbank/GenbankSearch.html
Text and similarity searching, provided by the National Center for Biotechnology Information (NCBI).

Sequence Analysis (Bielefeld University Bioinformatics Server) - http://bibiserv.techfak.uni-bielefeld.de/intro/seqdept.html
Collection of sequence analysis tools.

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.

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.

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.

Systems Biology of Photosynthesis - http://www.e-photosynthesis.org
Open web platform for modeling and reverse engineering of photosynthetic dynamism.

TFM Explorer - http://bioinfo.lifl.fr/TFM-Explorer/
Scans sequences for potential Transcription Factor binding sites using Patser and TRANSFAC.

Transcription Element Search Software (TESS) - http://www.cbil.upenn.edu/cgi-bin/tess/tess
Very helpful software for locating and displaying transcription factor binding sites within DNA sequences - from the Univ. of Penn.

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.

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.

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.

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.

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.

Zinc Finger Tools - http://www.scripps.edu/mb/barbas/zfdesign/zfdesignhome.php
Helps users design zinc finger transcription factors.

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