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
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
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
