Sequence Reformatting

• BIMCORE:  ReadSeq (N/A) sequence conversion program

Translation

• DNA sequence translation

Restriction Site Mapping

• WebCutter online restriction enzyme mapping facility

RNA Secondary Structure

• RNA secondary structure prediction
• SStructView: RNA SECONDARY STRUCTURE VIEWER APPLET

Pattern Recognition

• SignalScan Signal Scan for homology to signal sequences.
• TransFac: Transcription Factor Database Search
• TFFACTOR and TFSITE Transcription Factor Data at EMBL-Heidelberg

Pairwise Comparison

• DotPlot
• BCM: Pairwise Sequence Alignment

Multiple Sequence Alignments

• BIMCORE: ClustalW
• BCM: Multiple Sequence Alignments

Database Searching

• BCM Search Launcher at Baylor College of Medicine
• BLAST Basic Local Alignment Research Tool at NCBI
• SRS 6 Multiple Database Search Launcher at EBI

• GeneMark Gene Predicition using Hidden Markov Models (HMMs)
• Gene Finder Predict Gene Structure, Internal Exons and Splicing Sites in DNA and Exon-Exon Junstion in cDNA at Baylor College of Medicine
• Grail Analysis of the Protein Coding Potential of a DNA Sequence

Protein Secondary Structure Prediction

• Coils Prediction of Coiled Coil Regions in Protein Sequences at ISREC, Switzerland
• BLOCKS Database of Highly Conserved Regions in Proteins at Fred Hutchinson Cancer Research Center
• DSSP Database of Secondary Structure of Proteins from PDB at EMBL-Heidelberg
• FSSP Database of Families of Structurally Similar Proteins derived from PDB at EMBL-Heidelberg
• HSSP Database of Homology-Derived Structures of Proteins based on PDB and SwissProt at EMBL
• PHD Predict Protein Secondary Structure at EMBL-Heidelberg
• PredictProtein Predict Protein Secondary Structure at EMBL-Heidelberg
• ProDom A Protein Domain Database and ProDom-Search at INRA-Toulouse, France
• PSORT Predict Protein Sorting Signals Coded in Amino Acid Sequences at GenomeNet, Japan
• PSSP Protein Secondary Structure Prediction at Baylor College of Medicine
• SWISSDOM SwissProt Entries in a ProDom Map at EBI

• Amino Acid Comp Analysis Protein Identification in SwissProt and PIR using Amino Acid Composition at EMBL-Heidelberg
• ProFound Search known protein sequences with peptide mass information.
• PepFrag Search known protein sequences with peptide fragment mass information.
• Mascot Peptide Mass Fingerprint Search

Modeling

• Swiss-Model Automated Protein Modelling at ExPASy, Switzerland
• NRL_3D Sequence/Structure Database derived from PDB at Johns Hopkins
• PDB-Browser Protein Data Bank Structures at Brookhaven National Laboratory