Bioinformatics Tools

Field of Interest Type of Analysis Sought More Specifically (if possible)

Notes:
  • - Most of the information provided on this page is copied from the related linked pages in an effort to provide the descriptions the linked sites use for themselves rather than my own interpretation of the site.
  • - These links to internal and external sites are assembled here for your convenience and are provided by the generosity of others, please remember to properly acknowledge and reference any services you make use of.
  • - It is important to remember that many sites provide conceptual assignments and models, not experimental results!
     
  • - Please let me know which sites you find useful, and which you find less-so. This will help me know what to maintain in the database of sites.
     
   
CBS Prediction ServersCenter for Biological Sequence Analysis (CBS) Prediction Servers

Nucleotide Sequences

  • EasyGene
    Genes in prokaryotes.
  • GeneMachine
    Analysis of DNA microarray data.
  • GenomeAtlas
    DNA structural atlases for complete chromosomes and genomes.
  • HMMgene
    Genes in eukaryotes.
  • NetGene2
    Intron splice sites in human, C. elegans and A. thaliana DNA.
  • NetPlantGene
    Intron splice sites in Arabidopsis thaliana DNA.
  • NetStart
    Translation start in vertebrate and A. thaliana DNA.
  • OligoWiz
    Design of oligonucleotides for DNA microarrays.
  • Promoter
    Transcription start sites in vertebrate DNA.

Amino Acid Sequences

  • ArchaeaFun
    Enzyme/non-enzyme and enzyme class (Archea).
  • ChloroP
    Chloroplast transit peptides and their cleavage
    sites in plant proteins.
  • CPHmodels
    Protein structure from sequence: distance constraints.
  • DictyOGlyc
    O-(alpha)-GlcNAc glycosylation sites
    (trained on Dictyostelium discoideum proteins).
  • distanceP
    Protein distance constraints.
  • NetChop
    Proteasomal cleavages (MHC ligands).
  • NetNGlyc
    N-linked glycosylation sites in human proteins.
  • NetOGlyc
    O-GalNAc (mucin type) glycosylation sites in mammalian proteins.
  • NetPhos
    Serine, threonine and tyrosine phosphorylation
    sites in eukaryotic proteins.
  • NetPicoRNA
    Posttranslational cleavage by picornaviral proteases.
  • ProtFun
    Protein functional category and enzyme class (Eukarya).
  • RedHom
    Reduction of sequence similarity in a data set.
  • SignalP
    Signal peptide and cleavage sites in gram+,
    gram- and eukaryotic amino acid sequences.
  • TargetP
    Subcellular location of proteins: mitochondrial,
    chloroplastic, secretory pathway, or other.
  • TMHMM
    Transmembrane helices in proteins.
  • YinOYang
    O-(beta)-GlcNAc glycosylation and Yin-Yang sites
    (intracellular/nuclear proteins).
DBGETDBGET - Integrated database retrieval system
EBIThe EMBL Outstation - European Bioinformatics Institute (EBI) is a centre for research and services in bioinformatics. The Institute manages databases of biological data including nucleic acid, protein sequences and macromolecular structures.
ToolboxDatabases
EMBLEMBL: European Molecular Biology Laboratory.
Actually there are several "outstations", each with there own launch sites. Included is the European Bioinformatics Institute (EBI) - a centre for research and services in bioinformatics. The Institute offers a wealth of information and tools - far too many to list and link individually here, but including:
Database Services for biological data (Nucleotide Sequences, Protein Sequences, Sequence Structure Classifications, Macromolecular Structures, Sequence Mapping, Archives) and
Database Searching, Browsing and Analysis Tools(Database Searching, Homology Searches [DNA and Protein], Specialised Servers, 3D Structure Analysis, Other Analysis Tools and Utilities).
EMBNetThe Swiss node of the European Molecular Biology Network. EMBnet is a science-based group of collaborating nodes throughout Europe -and a number of nodes outside Europe-. The combined expertise of the nodes allows EMBnet to provide services to the European molecular biology community which encompasses more than can be provided by a single node.
Services include -
  • Basic BLAST (Sequence searches)
  • Advanced BLAST (Sequence searches)
  • FDF (Sequence searches by Smith-Waterman algorithm)
  • TMPRED (Transmembrane regions detection)
  • LALIGN (Alignments of 2 sequences)
  • PRSS (Optimal score of an alignment)
  • COILS (Coiled domains prediction)
  • BOXSHADE (Multiple alignments designer)
  • ClustalW (Multiple sequence alignment)
  • T-COFFEE (Multiple sequence alignment)
  • SRS6 (searches at SIB-Lausanne)
  • Fetch (get sequences)
ISREC bioinformaticsresources include:
  • Hits (a database and web tools devoted to protein domains)
  • ESTScan (Search DNA sequences for coding regions)
  • Dotlet (a Java applet for dotmatrix sequence comparisons [best viewed on Win95/NT and Linux])
  • PFSCAN (Profile searches)
  • PFRAMESCAN (Frame tolerant Profile searches)
  • PSTSCAN (Search the PROSITE database with a protein sequence)
  • SAPS (Statistical analysis of protein sequences), PatternFind (Search a protein database with a pattern)
  • EPD (Eukaryotic Promoter Database)
  • FTP server (Databases and softwares).
EMBOSSEMBOSS suite of Bioinformatics Programs
EMBOSS provides many/most of the bioinformatics tools available in the GCG package.
Ensembl Genome BrowserEnsembl Genome Browser
Ensembl presents up-to-date sequence data and the best possible automatic annotation for eukaryotic genomes. Available now are human, mouse and Drosophila. Others will be added soon.
EntrezEntrez is a retrieval system for searching several linked databases. It provides access to:
  • PubMed: The biomedical literature(PubMed)
  • Nucleotide sequence database(Genbank)
  • Protein sequence database
  • Structure: three-dimensionalmacromolecular structures
  • Genome: complete genomeassemblies
  • PopSet: population study datasets
  • OMIM: OnlineMendelian Inheritance in Man
  • Taxonomy:organisms in GenBank
  • Books: online books
  • ProbeSet: gene expression and microarray datasets
  • 3D Domains: domains from Entrez Structure
  • UniSTS: markers and mapping data
  • SNP: single nucleotide polymorphisms
  • CDD: conserved domains
  • Pre-computed similarity searches are available for most databaserecords producing a list of related sequences, structure neighbors, as well as related articles.
ExPASyExpert Protein Analysis System (ExPASy) proteomics server of the Swiss Institute of Bioinformatics (SIB). This server is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE. This site offers access to:
Databases -Tools and Software Packages -
  • Proteomics tools (Identification and characterization , DNA -> Protein, Similarity searches, Pattern and profile searches, Post-translational modification prediction, Primary structure analysis, Secondary structure prediction, Tertiary structure, Transmembrane regions detection, Alignment)
  • Melanie 3 (Software for 2-D PAGE analysis)
  • SWISS-MODEL (Automated knowledge-based protein modelling server), Swiss-PdbViewer (tool for structure display and analysis)
  • Boehringer Mannheim's Biochemical Pathways.
Also available at ExPASy
GeneCards?GeneCards? is a database of human genes, their products and their involvement in diseases. It offers concise information about the functions of all human genes that have an approved symbol, as well as selected others [complete gene list] [disease genes] .
GeneLynxGeneLynx is a portal to a collection of hyperlinks for each human gene. It is implemented as an easily extensible relational database with a straightforward user interface.
You can access the information about a particular human gene by providing any reasonable identifier - just type a keyword, ANY accession number or ID below, or submit a related protein or nucleotide sequence on the BLAST search page. You can also perform a more refined keyword search on the Text search page.
GenomeNetGenomeNet is a Japanese network of database and computational services for genome research and related research areas in molecular and cellular biology. GenomeNet was established in September 1991 under the Human Genome Program of the then Ministry of Education, Science and Culture (Monbusho). The GenomeNet service is operated by the Bioinformatics Center, Institute for Chemical Research (ICR), Kyoto University with supports from the Ministry of Education, Culture, Sports, Science and Technology (Monkasho).
GenomeNet Genome Services -GenomeNet Database Services -
  • KEGG (Kyoto Encyclopedia of Genes and Genomes) includes
    • PATHWAY (Pathways and complexes)
    • GENES (Gene annotations)
    • GENOME (Genome maps)
    • SSDB (Precomputed sequence similarities)
    • EXPRESSION (Microarray gene expression profiles)
    • BRITE (Biomolecular Relationsin Information Transmissionand Expression; Protein-protein interactions and relations)
    • LIGAND (Chemical compounds and reactions)
    • BLAST/FASTA (Search against GENES or GENOME)
  • DBGET/LinkDB Integrated Database Retrieval System includes
  • Sequence Interpretation Tools -
    • BLAST (Sequence similarity search)
    • FASTA (Sequence similarity search)
    • MOTIF (Sequence motif search)
    • CLUSTALW (Multiple sequence alignment).
Genomics & Bioinformatics GroupThe Genomics & Bioinformatics Group (GBG) web site offers useful bioinformatic program packages, microarray data analysis information, and molecular databases for genomic and proteomic research.

Available bioinformatic resources from the GBG (The Miner Suite) include:

Available molecular databases on the NCI-60 cancer cells include:

Helmholtz Network for BioinformaticsThe Helmholtz Network for Bioinformatics is a user-friendly web interface for integrating complex bioinformatics tasks. It is a joint venture of leading German bioinformatics research groups and offers convenient access to numerous bioinformatics resources through a single web portal.
Registration: For using the HNB service it is necessary that you register yourself using the registration form. You will receive an email with your personal HNB user certificate, which must be installed in your web browser.
InterProInterPro (EMBL) - InterPro was built from a collection of databases (Pfam 6.0, PRINTS 30.0, PROSITE 16.35, ProDom 2001.1, SMART 3.1 and the current SWISS-PROT + TrEMBL data) providing a powerful tool that integrates information from a variety of sources.
NCBINational Center for Biotechnology information at the NIH. NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information - all for the better understanding of molecular processes affecting human health and disease. NCBI provides access to:Including:
  • GenBank - Database of Nucleic Acid and Protein sequences.
TIGRTIGR: The Institute for Genomic Research
Founded in 1992, The Institute for Genomic Research (TIGR) is a not-for-profit research institute whose primary research interests are in structural, functional and comparative analysis of genomes and gene products from a wide variety of organisms including viruses, eubacteria (both pathogens and non-pathogens, archaea (the so-called third domain of life), and eukaryotes (plants, animals, fungi and protists such as the malarial parasite).
VirgilDatabase of rich links.
Virgil is a database of rich links for data browsing, data analysis and database interconnection, with a focus on human data. It contains more than 40,000 rich links from 5 major databases: SWISS-PROT, GenBank, PDB, GDB and OMIM.
Virgil uses an object-oriented database engine: Eyedb. Virgil data model was designed to comprehensively describe a link between two biological objects.


Bioinformatics
Fox Chase Cancer Center
Phone: (215) 728-3660