Which analyses need to be run?

• Similarity searches

  • BLAST (Altschul et al., 1990)
    • BLASTN (nucleotide databases)
    • BLASTX (amino acid databases)
    • TBLASTX (amino acid databases, six-frame translation)
  • sim4 (Miller et al., 1998)
    • Sequence alignment program for finding near-perfect matches between nucleotide sequences containing introns

• Gene predictors

  • Genefinder (Green, unpublished)
  • GenScan (Burge and Karlin, 1997)
  • Genie (Reese et al., 1997)

• Other analyses

  • tRNAscanSE (Lowe and Eddy, 1996)

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