Tomato Genetics and Breeding Program       

Internet Tools for Sequence Analysis            

David Francis and Sophien Kamoun

• Plant Genome Databases European Mirror (INRA)
• Genetic Resources Information Network (GRIN)
• Solanacaea Genome Network

• 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)
  • ClustalW at EBI Tools

• 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.bioinformatics.org/JaMBW/