Programs in the FastA3 Package

• FastA3 - Compare a protein sequence to a protein database, or a DNA sequence to a DNA database, using the FastA algorithm. Search speed and selectivity are controlled with the ktup (word-size) parameter. Searches with ktup=1 are slower, but more sensitive, while ktup=2 is faster but less effective.
  For proteins, the default is ktup=2. For DNA, the default is ktup=6. Use ktup=3 or ktup=4 more sensitivity. Use ktup=1 for oligonucleotides (length < 20).
• Ssearch3 - Compare a protein sequence to a protein database, or a DNA database, using the Smith-Waterman algorithm. It is very slow but much more sensitive for full-length proteins comparison.
• Fastx3 - Compare a DNA sequence to a protein database, by comparing the translated DNA sequence in three frames and allowing gaps and frameshifts.