Internet Tools for Sequence Analysis

David Francis and Sophien Kamoun

• Agricultural Genome Information System
• Plant Genome Databases
• Genetic Resources Information Network (GRIN)

• National Center for Biotechnology Information
• The Institute for Genomics Research (TIGR)
• The TIGR tomato gene index
• Structural Classification of Proteins (SCOP)
• Searching GenBank
• Entrez Browser
• BLAST sequence similarity searching

• Similarity Search
• Nucleic acid vs Nucleic acid (BLASTn)
• Amino acid vs Amino acid (BLASTp)
• Nucleic acid vs Amino acid (BLASTx)
• Structural Classification of Proteins (SCOP)
• Alignment
• BLAST 2 sequences
• Baylor College of Medicine Search Launcher
• Multiple Sequence Alignments (ClustalW)

• Sequence utilities
• Open Reading Frame (ORF) Finder

Proteomics and Peptide Sequence Identification

• Protein Prospector
• Protein Prospector - Homology
• Matrix Science

Restriction Enzyme Analysis

• Restriction Enzyme Mapping NEB
• Web Cutter

Primer Design for PCR

• http://www-genome.wi.mit.edu/cgi-bin/primer/primer3_www.cgi
• http://www.embl-heidelberg.de/~toldo/JaMBW/5/2/