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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/
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/
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/L...
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/
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/
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/
ERGO
Online service integrating biological data from genomics, biochemistry, genetics and high-throughput expression profiling, to achieve a comprehensive pattern-based analysis of genes and genomes.
http://ergo.integratedgenomics.com/ERGO/
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/
Bioverse
Provides a framework for exploring the relationships among the molecular, genomic, proteomic, systems, and organismal worlds.
http://bioverse.compbio.washington.edu
Virtual Genome Center
Online computational resources for PCR primer selection, similarity searching- from the Univ. of Minnesota.
http://alces.med.umn.edu/VGC.html
Bacterial Identification
Service for the identification of bacteria and fungi sequences by sequence alignment.
http://pbil.univ-lyon1.fr/bibi/query.php
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
MedMiner
An Internet biomedical data-mining tool for organizing search information gathered from textual or genetic databases - from the NIH National Cancer Inst.
http://discover.nci.nih.gov/textmining/mai...
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/
Information Génomique et Structurale (CNRS)
Online services including T-Coffee, El-Nemo, Casper and FeeBack.
http://igs-server.cnrs-mrs.fr
LongTrace DNA Sequencing Service
Commercial service for improving the read length and quality of ABI 3730 DNA sequencing traces through reprocessing of the raw signal data. Free trial provided.
https://longtrace.nucleics.com
Gene Network Reconstruction
Reconstruction of gene regulatory networks from time-series microarray expression data sets.
http://bioinfo.phys.sinica.edu.tw
My Genomics Resource Centre
A Malaysian Genomics toolset for high-throughput analysis of biological data. Must register to use.
http://www.mgrc.com.my
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/
PANDORA
Protein ANnotation Diagram ORiented Analysis service that extracts biological information from user supplied sequences.
http://www.pandora.cs.huji.ac.il
Biomolecular Interaction Network Database (BIND)
BIND is a database designed to store full descriptions of interactions, molecular complexes and pathways.
http://bind.ca
JustBio: Online Tool Set
A Suite of Online tools for analysis of DNA/RNA, Proteins, and Arrays.
http://www.justbio.com/tools.php
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
CAP Sequence Assembler
DNA sequence assembly and contig formation.
http://bio.ifom-firc.it/ASSEMBLY/assemble....
InstaSeq
Google-based search engine for DNA, RNA or Protein sequences.
http://bioinformatics.georgetown.edu/Insta...
Carnac
A free software tool for analysing the hypothetical secondary structure of a family of homologous RNA.
http://bioinfo.lifl.fr/carnac/
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...
GenomeSURF
Colorful visualization of Sequence Frequency. Includes Human and Mouse Genomic Sequences. Evaluate uniqueness of graphically.
http://surf.gi.k.u-tokyo.ac.jp
FIE (5' end Information Extraction)
Gene sequence extraction of regions around the 5'-end (promoter) and/or the translation initiation site (TIS) of a gene.
http://sdmc.lit.org.sg/FIE/
Web Services at Institute of Microbial Technology, Chandigarh, India
Protein structure prediction (Protein Structural Classes, Secondary Structure Prediction), immunological methods (ProPred), genomics & 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
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
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/
Sequence Analysis (Bielefeld University Bioinformatics Server)
Collection of sequence analysis tools.
http://bibiserv.techfak.uni-bielefeld.de/i...
Entrez Browser
Retrieves molecular biology data and bibliographic citations from the NCBI's integrated databases.
http://www.ncbi.nlm.nih.gov/Entrez/
Systems Biology of Photosynthesis
Open web platform for modeling and reverse engineering of photosynthetic dynamism.
http://www.e-photosynthesis.org
General Repository for Interaction Datasets (GRID)
The GRID is a 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://biodata.mshri.on.ca/grid/servlet/In...
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...
Transterm - a database of mRNA regions and motifs
Transterm - an 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
QualTrace DNA Sequencing
A free online version of the QualTrace DNA sequencing software for quality control analysis of ABI 3730 & 3730xl traces files.
http://www.nucleics.com/qualtrace-dna-sequ...
Kangaroo
Search for motifs and paterns within amino acid and nucleotide databases
http://www.blueprint.org/products/kangaroo...
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/
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/
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
PEDANT
Completely automatic and exhaustive analysis of protein sequence sets - from individual sequences to complete genomes
http://pedant.gsf.de/
Gene and Protein Synonyms DataBase
Free service for retrieving all synonyms for a given gene or protein name.
http://biomint.pharmadm.com
TFM Explorer
Scans sequences for potential Transcription Factor binding sites using Patser and TRANSFAC.
http://bioinfo.lifl.fr/TFM-Explorer/
Ascidian Network
An online database able to relate expression data with other data such as lineage, induction, cell fates, genomic information, blastomere position and morphology in the developing ascidian embryo.
http://aniseed-ibdm.univ-mrs.fr
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
GenBank
Text and similarity searching of the GenBank sequence database provided by the National Center for Biotechnology Information (NCBI).
http://www.ncbi.nlm.nih.gov/Genbank/Genban...
Canadian Bioinformatics Help Desk
We provide bioinformatics support, services, servers, and software to Canadian researchers.
http://gchelpdesk.ualberta.ca
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
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
Center for Biological Sequence Analysis
Offers more than 30 online services for DNA and protein bioinformatics analysis.
http://www.cbs.dtu.dk/services/
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/
The Protein Information Resource
In collaboration with the Munich Information Center for Protein Sequences (MIPS) and the Japanese International Protein Sequence Database (JIPID) maintains the PIR-International Protein Sequence Database --- a comprehensive, annotated, and non-redundant set of protein sequence databases in which entries are classified into family groups and alignments of each group are available.
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/PlasMap...
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.ht...
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
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/
Genepop on the Web
Online version of the program for populational genetics.
http://wbiomed.curtin.edu.au/genepop/
ReadSeq
Converts amino acid and nucleotide sequence data formats including FASTA, GenBank, Phylip and others.
http://bimas.dcrt.nih.gov/molbio/readseq/
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2006