Bioinformatics Tools on the Web

Primary Structure Analysis

• ProtPram : Calculate physico-chemical parameters of a protein sequence (amino-acid and atomic compositions, pI, extinction coefficient, etc.) (ExPASy)
• The Sequence Manipulation Suite: A collection of JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences

Sequence Similarity

• Pairwise BLAST : (Similarity Search between Two Sequences)
• BLAST : Sequence Database Search Tool (NCBI)
• FASTA : Protein Sequence Database Search Tool (NPSA)

Multiple Sequence Alignment

• Clustal W : at European Bioinformatics Institute, EMBL
• Clustal W - Proteins : at Network Protein Sequence Analysis
• Clustal W - DNA : at NPSA

Phylogenetic Tree Construction

• Phylip programs

Structural Alignment

• DALI : Structural Similarity Tool
• FSSP : Fold classification based on Structure alignment of Proteins

Secondary Structure Prediction

• PredictProtein - Secondary Structure Prediction Tool
• PHD : PHD Secondary Structure Prediction Method at NPSA
• SOPMA : SOPMA Secondary Structure Prediction at NPSA

Advanced Primary Structure Analysis

• ExPASy : Proteomics Tools
• EMBL-European Bioinformatics Institute
• Pfam : Protein families database of Alignments and HMMs (Sanger)
• PatScan : Scan Sequence Database for Patterns
• PattinProt : Pattern Search at NPSA
• Profile Scan : Motif Search in a Protein Sequence
• Scan Prosite : Search Protein Sequence for Profiles at Prosite
• SMART : Simple Modular Architechture Research Tool at EMBL

Homology Modeling

• Swiss-Model : Homology Modeling Tool

Other Useful Links

• Spectroscopy Resource
• GENSCAN : Protein Prediction Tool
• Multicoil : Predicts location of coiled-coilregions in protein sequence
• BCM-HGSC : Human Genome Sequencing Center, Baylor College
• DOE-MBI : Useful Resource at the Structural Biology Lab, UCLA