Fast-All (pronounced fast-aye) a program for pairwise sequence alignment.
FASTA (pronounced FAST-Aye) stands for FAST-All, reflecting the fact that it can be used for a fast protein comparison or a fast nucleotide comparison. This program achieves a high level of sensitivity for similarity searching at high speed. This is achieved by performing optimised searches for local alignments using a substitution matrix. The high speed of this program is achieved by using the observed pattern of word hits to identify potential matches before attempting the more time consuming optimised search. The trade-off between speed and sensitivity is controlled by the ktup parameter, which specifies the size of the word. Increasing the ktup decreases the number of background hits. Not every word hit is investigated but instead initially looks for segment's containing several nearby hits.
An algorithm for identifying sequence similarities.
A database search tool used to compare a nucleotide or peptide sequence to a sequence database.
Program used to search simultaneously both protein and DNA sequence databases (Pearson and Lipman, 1988). FASTA uses a fast search to initially identify sequences with a high degree of similarity to the query sequence and then conducts a second comparison on the selected sequences. FASTA is slower than BLAST, but is more sensitive/sometimes yields different results.
a common single and also a sequential multiple sequence format
a simple format for holding sequences, and the example here is from the EMBL distribution ( hsinsu
A computer program based on the method of W. Pearson and D. Lipman [ Proc. Natl. Acad. Sci. U.S.A. 85, 2444-2448 (1988)] to search for similarities between one sequence (the query) and any group of sequences (the database).
The first widely used algorithm for database similarity searching. The program looks for optimal local alignments by scanning the sequence for small matches called "words". Initially, the scores of segments in which there are multiple word hits are calculated ("init1"). Later the scores of several segments may be summed to generate an "initn" score. An optimized alignment that includes gaps is shown in the output as "opt". The sensitivity and speed of the search are inversely related and controlled by the "k-tup" variable which specifies the size of a "word". ( Pearson and Lipman)
An alignment program for protein sequences created by Pearson and Lipman in 1988. The program is one of the many heuristic algorithms proposed to speed up sequence comparison. The basic idea is to add a fast prescreen step to locate the highly matching segments between two sequences, and then extend these matching segments to local alignments using more rigorous algorithms such as Smith-Waterman.
a format for listing DNA sequence, where the first line has descritive information followed on the next line by the sequence without numbering.
FASTA is a DNA and Protein sequence alignment software package first described (as FASTP) by David J. Lipman and William R. Pearson in 1985 in the article http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2983426 Rapid and sensitive protein similarity searches.