Resources in The Internet
Freeware and Web Sites
WebGene
 TOOLS FOR PREDICTION AND
ANALYSIS OF PROTEIN-CODING GENE
STRUCTURE
Samuel Karlin Group Web Server
 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.
• Structural and functional aspects of proteins (EMOTIF,
EMATRIX, and 3MOTIF).
• These methods can be used for assigning functions to
unidentified genomic sequences (Genomes).
• Accurate and rapid methods for comparing protein
structures and structural database search (LOCK and
3DSEARCH).
Biological Software
 Dr. Andrew C.R. Martin's bioinformatics




site
OpenRasMol
RasMol Home Page
SDSC Biology
Software+molbio-Listings
Education
 BioComputing Hypertext Coursebook
 Bioinformatics and Genomics 326 Schedule
 Nucleic Acids Research
 Perl Programming Course for Bioinformatics
and Internet
 Protein Threading
Gene Identification
 AG BIODV Software Development for
Molecular Biology
 argon.cshl.org-genefinder
 Censor Server Data Entry Form - Genetic
Information Research Institute
 GeneMark (TM) - Gene prediction
software programs
Molecular Modeling
 Center for Molecular Modeling
 Welcome to Gromacs
 3D-Dock Suite
Proteiomics
 ExPASy Molecular Biology Server
 GeneProt
 The ProDom protein domain database
 The Protein Data Bank
 The RCSB Protein Data Bank
Sequence analysis











BCM Search Launcher Multiple Sequence Alignments
Blocks WWW Server
Form for Multiple Sequence Alignment
IBM Bioinformatics and Pattern Discovery Group MUSCA Multiple Sequence Alignment
INFOBIOGEN Home Page
MEME - Motif Discovery and Search
Multalin interface page
Services for molecular biology computing
WebGene Home Page
Working Group Bioinformatics
Webcutter 2.0
Restriction Map -- Web 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
Input file name
Input Accession number or
gi number
Structure Prediction
 A Threader, LIBRA (Program for Protein
Structure Prediction)
 I-sites Library Home
 nnpredict input form
Databases and Others

























Algorithms, thermodynamics and databases for RNA secondary structure.
Bayesian Bioinformatics at Wadsworth Center
Bioinformatics (Computational Biology) at UC Santa Cruz
DDBJ homepage
EBI, the European Bioinformatics Institute (EMBL Outstation, Hinxton, UK) serving the bioinformatics community
EMBL - European Molecular Biology Laboratory
EMBL Monterotondo Mouse Biology Programme
EMBL Outstation, Hinxton, UK
ENDscript
ESPript
FASTA Programs
Genomatix MatInspector registration
Home Page - Genetic Information Research Institute
http--www.embl-hamburg.dehttp--www.genome.ad
Michael Zuker's Home Page
National Bioinformatics Institute
NCBI HomePage
Pittsburgh Supercomputing Center
Samuel Karlin Group Web Server
The Brutlag Bioinformatics Group
The EMBL Grenoble WWW page
The EMBL-Heidelberg PROPSEARCH Server
The FOLD-X server
The Protein Data Bank