1. Resources in The Internet Freeware and Web Sites

2. WebGene TTTTOOLS FOR PREDICTION AND ANALYSIS OF PROTEIN-CODING GENE STRUCTURE

3. Samuel Karlin Group Web Server Samuel Karlin Group Web Server TTTThe main research focus of the group concerns the development of mathematical and computational techniques and tools for the analysis of DNA and protein sequences.

4. Structural and functional aspects of proteins (EMOTIF, EMATRIX, and 3MOTIF).Structural and functional aspects of proteins (EMOTIF, EMATRIX, and 3MOTIF).EMOTIF EMATRIX3MOTIFEMOTIF EMATRIX3MOTIF These methods can be used for assigning functions to unidentified genomic sequences (Genomes).These methods can be used for assigning functions to unidentified genomic sequences (Genomes).Genomes Accurate and rapid methods for comparing protein structures and structural database search (LOCK and 3DSEARCH).Accurate and rapid methods for comparing protein structures and structural database search (LOCK and 3DSEARCH).LOCK 3DSEARCHLOCK 3DSEARCH

5. Biological Software  Dr. Andrew C.R. Martin's bioinformatics site Dr. Andrew C.R. Martin's bioinformatics site Dr. Andrew C.R. Martin's bioinformatics site  OpenRasMol OpenRasMol  RasMol Home Page RasMol Home Page RasMol Home Page  SDSC Biology SDSC Biology SDSC Biology  Software+molbio-Listings Software+molbio-Listings

6. Education  BioComputing Hypertext Coursebook BioComputing Hypertext Coursebook BioComputing Hypertext Coursebook  Bioinformatics and Genomics 326 Schedule Bioinformatics and Genomics 326 Schedule Bioinformatics and Genomics 326 Schedule  Nucleic Acids Research Nucleic Acids Research Nucleic Acids Research  Perl Programming Course for Bioinformatics and Internet Perl Programming Course for Bioinformatics and Internet Perl Programming Course for Bioinformatics and Internet  Protein Threading Protein Threading Protein Threading

7. Gene Identification  AG BIODV Software Development for Molecular Biology AG BIODV Software Development for Molecular Biology AG BIODV Software Development for Molecular Biology  argon.cshl.org-genefinder argon.cshl.org-genefinder  Censor Server Data Entry Form - Genetic Information Research Institute Censor Server Data Entry Form - Genetic Information Research Institute Censor Server Data Entry Form - Genetic Information Research Institute  GeneMark (TM) - Gene prediction software programs GeneMark (TM) - Gene prediction software programs GeneMark (TM) - Gene prediction software programs

8. Molecular Modeling  Center for Molecular Modeling Center for Molecular Modeling Center for Molecular Modeling  Welcome to Gromacs Welcome to Gromacs Welcome to Gromacs  3D-Dock Suite 3D-Dock Suite 3D-Dock Suite

9. Proteiomics  ExPASy Molecular Biology Server ExPASy Molecular Biology Server ExPASy Molecular Biology Server  GeneProt GeneProt  The ProDom protein domain database The ProDom protein domain database The ProDom protein domain database  The Protein Data Bank The Protein Data Bank The Protein Data Bank  The RCSB Protein Data Bank The RCSB Protein Data Bank The RCSB Protein Data Bank

10. Sequence analysis  BCM Search Launcher Multiple Sequence Alignments BCM Search Launcher Multiple Sequence Alignments BCM Search Launcher Multiple Sequence Alignments  Blocks WWW Server Blocks WWW Server Blocks WWW Server  Form for Multiple Sequence Alignment Form for Multiple Sequence Alignment Form for Multiple Sequence Alignment  IBM Bioinformatics and Pattern Discovery Group - MUSCA Multiple Sequence Alignment IBM Bioinformatics and Pattern Discovery Group - MUSCA Multiple Sequence Alignment IBM Bioinformatics and Pattern Discovery Group - MUSCA Multiple Sequence Alignment  INFOBIOGEN Home Page INFOBIOGEN Home Page INFOBIOGEN Home Page  MEME - Motif Discovery and Search MEME - Motif Discovery and Search MEME - Motif Discovery and Search  Multalin interface page Multalin interface page Multalin interface page  Services for molecular biology computing Services for molecular biology computing Services for molecular biology computing  WebGene Home Page WebGene Home Page WebGene Home Page  Working Group Bioinformatics Working Group Bioinformatics Working Group Bioinformatics  Webcutter 2.0 Webcutter 2.0 Webcutter 2.0

11. Restriction Map -- Web Cutter 2 Web Cutter 2Web Cutter 2  Rainbow cutters Highlight your favorite enzymes in color or boldface for easy at-a-glance identification  Silent cutters Find sites which may be introduced by silent mutagenesis of your coding sequence  Sequence uploads Input sequences directly into Webcutter from a file on your hard drive without needing to cut-and-paste  Degenerate sequences Analyze restriction maps of sequences containing ambiguous nucleotides like N, Y, and R.  Circular sequences Choose whether to treat your sequence as linear or circular  Enzyme info Click into the wealth of references and ordering information at New England BioLabs' REBASE, directly from your restriction map results

12. Input file name Input Accession number or gi number

14. Structure Prediction  A Threader, LIBRA (Program for Protein Structure Prediction) A Threader, LIBRA (Program for Protein Structure Prediction) A Threader, LIBRA (Program for Protein Structure Prediction)  I-sites Library Home I-sites Library Home I-sites Library Home  nnpredict input form nnpredict input form nnpredict input form

15. Databases and Others  Algorithms, thermodynamics and databases for RNA secondary structure. Algorithms, thermodynamics and databases for RNA secondary structure. Algorithms, thermodynamics and databases for RNA secondary structure.  Bayesian Bioinformatics at Wadsworth Center Bayesian Bioinformatics at Wadsworth Center Bayesian Bioinformatics at Wadsworth Center  Bioinformatics (Computational Biology) at UC Santa Cruz Bioinformatics (Computational Biology) at UC Santa Cruz Bioinformatics (Computational Biology) at UC Santa Cruz  DDBJ homepage DDBJ homepage DDBJ homepage  EBI, the European Bioinformatics Institute (EMBL Outstation, Hinxton, UK) serving the bioinformatics community EBI, the European Bioinformatics Institute (EMBL Outstation, Hinxton, UK) serving the bioinformatics community EBI, the European Bioinformatics Institute (EMBL Outstation, Hinxton, UK) serving the bioinformatics community  EMBL - European Molecular Biology Laboratory EMBL - European Molecular Biology Laboratory EMBL - European Molecular Biology Laboratory  EMBL Monterotondo Mouse Biology Programme EMBL Monterotondo Mouse Biology Programme EMBL Monterotondo Mouse Biology Programme  EMBL Outstation, Hinxton, UK EMBL Outstation, Hinxton, UK EMBL Outstation, Hinxton, UK  ENDscript ENDscript  ESPript ESPript  FASTA Programs FASTA Programs FASTA Programs  Genomatix MatInspector registration Genomatix MatInspector registration Genomatix MatInspector registration  Home Page - Genetic Information Research Institute Home Page - Genetic Information Research Institute Home Page - Genetic Information Research Institute  http--www.embl-hamburg.de- http--www.embl-hamburg.de-  http--www.genome.ad http--www.genome.ad  Michael Zuker's Home Page Michael Zuker's Home Page Michael Zuker's Home Page  National Bioinformatics Institute National Bioinformatics Institute National Bioinformatics Institute  NCBI HomePage NCBI HomePage NCBI HomePage  Pittsburgh Supercomputing Center Pittsburgh Supercomputing Center Pittsburgh Supercomputing Center  Samuel Karlin Group Web Server Samuel Karlin Group Web Server Samuel Karlin Group Web Server  The Brutlag Bioinformatics Group The Brutlag Bioinformatics Group The Brutlag Bioinformatics Group  The EMBL Grenoble WWW page The EMBL Grenoble WWW page The EMBL Grenoble WWW page  The EMBL-Heidelberg PROPSEARCH Server The EMBL-Heidelberg PROPSEARCH Server The EMBL-Heidelberg PROPSEARCH Server  The FOLD-X server The FOLD-X server The FOLD-X server  The Protein Data Bank The Protein Data Bank The Protein Data Bank