Bioinformatics Sequence Analysis Tools

Below listed are few online Sequence Analysis tools. We regularly add new websites and new tools in Bioinformatics.
If you come accross new tools in bioinformatics, please let us know.

Sequence Analysis tools Online

Protein Sequence Analysis Tools

• 3DCrunch - Database Browser of modeled Swiss-Prot proteins at ExPASy, Switzerland
• 3D-Jigsaw - Comparative modeling server
• AAT - Analysis and Annotation Tool for finding genes in genomic sequences 
• ASC - Analytic Surface Calculation of PDB molecules @t EMBL, Heidelberg)
• BLOCKS Search - Search a protein against BLOCKS database
• BTPRED - Prediction of beta-turns
• CD-Search - Search a protein against CDD domain database
• Chime - Plugin for structure view
• Cn3D - Plugin for structure view for structure @ NCBI
• eMOTIF Search - Assign putative function to new proteins by sequence comparison with IDENTIFY motif database.
• Coils - Prediction of coiled Coil regions by Lupas method
• CPHmodels - Structure prediction by comparative homology modeling
• DIP - Search Database of Interacting Proteins
• DOMPLOT - Structural domain organization annotated by ligand contacts.
• eMATRIX Search - Predict function by sequence analysis using minimal-risk scoring matrices.
• eMOTIF Maker - Generate motifs describing protein families or superfamilies
• FingerPRINTScan - Search a protein sequence against protein motif fingerprints database
• HMMTOP - Prediction of transmembrane helices and topology of proteins
• JPred - Protein secondary structure prediction
• LIBRA - LIght Balance for Remote Analogous proteins: search compatible structure of a target sequence by threading
• Comparative modeling tools
• Modules - Mobile protein domains database
• MolSurfer - Calculate and navigate protein-protein interfaces
• NetOGlyc - Prediction of O-glycosylation sites in mammalian proteins
• nnPredict - Protein secondary structure prediction.
• PFSCAN - Protein search against different profile databases
• PPSearch - Search a protein sequence against prosite pattern database
• Predicting Protein 3D structure based on homologous sequence search
• RasMol - 3D viewer
• VAST - Structure-structure similarity search
• WebMol - 3D viewer

DNA / RNA Sequence Analysis

• Gene Finder -Exon and Splice Site Prediction
• GENEID -Prediction of Exons and Gene Structure
• ORD ID - Open Reading Frame search
• ORF Finder - Open Reading Frame Finder
• PatScan - DNA Sequence Motif search