Resources in The InternetResources in The InternetFreeware and Web SitesFreeware and Web Sites

WebGeneWebGene

TOOLS FOR PREDICTION AND TOOLS FOR PREDICTION AND ANALYSIS OF PROTEIN-CODING GENE ANALYSIS OF PROTEIN-CODING GENE STRUCTURE STRUCTURE

Samuel Samuel KarlinKarlin Group Web Server Group Web Server

The main research focus of the group The main research focus of the group concerns the development of concerns the development of mathematical and computational mathematical and computational techniques and tools for the analysis of techniques and tools for the analysis of DNA and protein sequences.DNA and protein sequences.

• Structural and functional aspects of proteins (Structural and functional aspects of proteins (EMOTIF, EMATRIX, and 3MOTIF).

• These methods can be used for assigning functions to These methods can be used for assigning functions to unidentified genomic sequences (unidentified genomic sequences (Genomes).

• Accurate and rapid methods for comparing protein Accurate and rapid methods for comparing protein structures and structural database search (structures and structural database search (LOCK and 3DSEARCH).

Biological SoftwareBiological Software

Dr. Andrew C.R. Martin's bioinformatics sitDr. Andrew C.R. Martin's bioinformatics sitee

OpenRasMolOpenRasMol RasMolRasMol Home Page Home Page SDSC BiologySDSC Biology Software+molbio-ListingsSoftware+molbio-Listings

EducationEducation

BioComputingBioComputing Hypertext Hypertext CoursebookCoursebook Bioinformatics and Genomics 326 ScheduleBioinformatics and Genomics 326 Schedule Nucleic Acids ResearchNucleic Acids Research Perl Programming Course for Bioinformatics anPerl Programming Course for Bioinformatics an

d Internetd Internet Protein ThreadingProtein Threading

Gene IdentificationGene Identification

AG BIODV Software Development for MolAG BIODV Software Development for Molecular Biologyecular Biology

argon.cshl.org-genefinderargon.cshl.org-genefinder Censor Server Data Entry Form - Genetic ICensor Server Data Entry Form - Genetic I

nformation Research Institutenformation Research Institute GeneMarkGeneMark

(TM) - Gene prediction software programs (TM) - Gene prediction software programs

Molecular ModelingMolecular Modeling

Center for Molecular ModelingCenter for Molecular Modeling Welcome to GromacsWelcome to Gromacs 3D-Dock Suite3D-Dock Suite

ProteiomicsProteiomics

ExPASyExPASy Molecular Biology Server Molecular Biology Server GeneProtGeneProt The The ProDomProDom protein domain database protein domain database The Protein Data BankThe Protein Data Bank The RCSB Protein Data BankThe RCSB Protein Data Bank

Sequence analysisSequence analysis BCM Search Launcher Multiple Sequence AlignmentsBCM Search Launcher Multiple Sequence Alignments Blocks WWW ServerBlocks WWW Server Form for Multiple Sequence AlignmentForm for Multiple Sequence Alignment IBM Bioinformatics and Pattern Discovery Group - MUSIBM Bioinformatics and Pattern Discovery Group - MUS

CA Multiple Sequence AlignmentCA Multiple Sequence Alignment INFOBIOGEN Home PageINFOBIOGEN Home Page MEME - Motif Discovery and SearchMEME - Motif Discovery and Search MultalinMultalin interface page interface page Services for molecular biology computingServices for molecular biology computing WebGene Home PageWebGene Home Page Working Group BioinformaticsWorking Group Bioinformatics Webcutter 2.0Webcutter 2.0

Restriction Map -- Restriction Map -- Web Cutter 2Web Cutter 2 Rainbow cutters Highlight your favorite enzymes in color Rainbow cutters Highlight your favorite enzymes in color

or boldface for easy at-a-glance identification or boldface for easy at-a-glance identification Silent cutters Find sites which may be introduced by sileSilent cutters Find sites which may be introduced by sile

nt mutagenesis of your coding sequence nt mutagenesis of your coding sequence Sequence uploads Input sequences directly into WebcuttSequence uploads Input sequences directly into Webcutt

er from a file on your hard drive without needing to cut-aer from a file on your hard drive without needing to cut-and-paste nd-paste

Degenerate sequences Analyze restriction maps of sequDegenerate sequences Analyze restriction maps of sequences containing ambiguous nucleotides like N, Y, and R.ences containing ambiguous nucleotides like N, Y, and R.

Circular sequences Choose whether to treat your sequeCircular sequences Choose whether to treat your sequence as linear or circular nce as linear or circular

Enzyme info Click into the wealth of references and ordeEnzyme info Click into the wealth of references and ordering information at New England BioLabs' REBASE, direring information at New England BioLabs' REBASE, directly from your restriction map resultsctly from your restriction map results

Input file name

Input Accession number or gi number

Structure PredictionStructure Prediction

A A ThreaderThreader, LIBRA (Program for Protein Structure Pre, LIBRA (Program for Protein Structure Prediction)diction)

I-sites Library HomeI-sites Library Home nnpredictnnpredict input form input form

Databases and OthersDatabases and Others Algorithms, thermodynamics and databases for RNA secondary structure.Algorithms, thermodynamics and databases for RNA secondary structure. Bayesian Bioinformatics at Wadsworth CenterBayesian Bioinformatics at Wadsworth Center Bioinformatics (Computational Biology) at UC Santa CruzBioinformatics (Computational Biology) at UC Santa Cruz DDBJ homepageDDBJ homepage EBI, the European Bioinformatics Institute (EMBL Outstation, EBI, the European Bioinformatics Institute (EMBL Outstation, HinxtonHinxton, UK) serving the bioinformatics community, UK) serving the bioinformatics community EMBL - European Molecular Biology LaboratoryEMBL - European Molecular Biology Laboratory EMBL EMBL MonterotondoMonterotondo Mouse Biology Mouse Biology ProgrammeProgramme EMBL Outstation, EMBL Outstation, HinxtonHinxton, UK, UK ENDscriptENDscript ESPriptESPript FASTA ProgramsFASTA Programs GenomatixGenomatix MatInspectorMatInspector registration registration Home Page - Genetic Information Research InstituteHome Page - Genetic Information Research Institute http--http--www.embl-hamburg.dewww.embl-hamburg.de-- http--http--www.genome.adwww.genome.ad Michael Michael Zuker'sZuker's Home Page Home Page National Bioinformatics InstituteNational Bioinformatics Institute NCBI NCBI HomePageHomePage Pittsburgh Supercomputing Center Pittsburgh Supercomputing Center Samuel Samuel KarlinKarlin Group Web Server Group Web Server The The BrutlagBrutlag Bioinformatics Group Bioinformatics Group The EMBL The EMBL GrenobleGrenoble WWW page WWW page The EMBL-Heidelberg PROPSEARCH ServerThe EMBL-Heidelberg PROPSEARCH Server The FOLD-X serverThe FOLD-X server The Protein Data BankThe Protein Data Bank