Fasta
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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.
Fasta
- 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