Analysis

Sequence Analysis tools

• READSEQ Sequence Conversion
• EMBOSS programs under Pise
• ORF Finder (Open Reading Frame Finder) @ NCBI
• BACKTRANSEQ : Back translate a protein sequence (EMBOSS)
  
  

Sequence Similarity Searches

• Basic Local Alignment Search Tool(BLAST) at NCBI
• Blast at EBI
• NCBI BLAST Search with Entrez and SRS Links
• ISREC WU-BLAST server
• Advanced BLAST2 Search with post-processing at EMBL
• FASTA homology searches
• BLITZ ultra-fast protein databases searches
• Sequence Interpretation Tools(GenomeNet WWW server- Japan)
• http://www.ebi.ac.uk/Tools/similarity.html

 

PROSITE pattern searches

• EBI
• EXPASY
• IBCP

 

Alignment

• ClustalW Multiple Sequence Alignment

 

Primary structure analysis

• HLA_Bind - Prediction of MHC type I (HLA) peptide binding
• SYFPEITHI - A DATABASE OF MHC LIGANDS AND PEPTIDE MOTIFS (Ver. 1.0)
• ProtParam - Physico-chemical parameters of a protein sequence (amino-acid and atomic compositions, pI, extinction coefficient, etc.)
• Antigenic : Find antigenic sites in proteins (EMBOSS)

 

Hydrophilicity/Hydrophobicity Search and Comparison

• Protein Hydrophilicity/Hydrophobicity Search and Comparison Server

 

Antibody Resources

• Antibody Resource Page
• AbCheck - Antibody Sequence tester

 

Other

• ExPASy Proteomics tools
• Network Protein Sequence analysis server NPS@ France 
• Genemark Program
• Codon Usage Tabulated from Genbank
• Compute pI/Mw tool
• BCM Gene Finder
• GeneQuiz server homepage
• GeneFIND Family Identification System (University of Texas Health Center at Tyler )
• Primer
• Signal Scan
• Promoter Scan
• TRANSFAC (-database sequence analysis tools)
• The CMS Molecular Biology Resource
• Computing applied to Biomolecules and Genomes , France
• Software Developed and Maintained by Dr. K. Sekar