FASTA is a program for rapidly aligning protein and DNA sequences. It searches for matching k-tuples or sequence words and builds a local alignment based on these matches. It identifies the 10 best matching regions through k-tuple screening, joins nearby matches, and finds the highest density regions. It generates longer regions of identity and recalculates scores, with INITN and OPT scores used to rank database matches. Sensitivity refers to the ability to locate distantly related family members with limited similarity.

1. Heuristic
Alignment

2. FASTA
A program for rapid alignment of pairs of protein and
DNA sequences
Searches for matching sequence patterns or words, called
k-tuples
The program then builds a local alignment based on
these word matches

4. Lookup method for finding an alignment

5. Location of 10 best matching
regions by rapid screen
i. Finding k consecutive
matches
ii. Joining of matches within a
certain distance
iii. Identification of regions
with highest density

6. Evaluation of highest-density
regions by scoring matrices
Identification highest scoring
regions (INIT1)

7. Generation of Longer regions of
identity of score INITN by
joining initial regions
When INITN reach certain
threshold the score is
recalculated to give OPT score
(by Smith-Waterman algorithm)
By improving the score
sensitivity increases
selectivity decreases

8. INITN and OPT scores are used to rank database matches
Versions of FASTA,
FASTA – Prot on Prot / DNA on DNA
TFASTA – Prot on DNA library
FASTF/FASTS – Peptide on Prot
TFASTF/TFASTS – Peptide on DNA
FASTX/FASTY – DNA on Prot

9. Sensitivity:
The ability of a search method to locate as many members
of a protein family as possible, including distant members of
limited sequence similarity

10. Sensitivity:
The ability of a search method to locate as many members
of a protein family as possible, including distant members of
limited sequence similarity