Instructions:

  1. Choose Reference genome from drop-down menu
  2. Select DataSet Type to search against different resource:
    • Ref Genome: Genomic sequences
    • Ref Transcript: Transcript cDNA sequences
    • Ref CDS: Transcript CDS sequences
    • Ref Proteome: Transcript protein amino acid sequences
  3. Choose proper BLAST program:
    • megablast is optimized for comparison of very similiar sequences, e.g. intraspecies paralogues
    • blastn is better suited for interspecies comparisons with a shorter word-size
    • tblastn for a standard protein-translated nucleotide comparison
    • blastn-short is optimized for sequences less than 30 nucleotides, e.g. primers
  4. Set e-value cutoff, the default one used here is 0.01, which is relaxed to include more hits