FASTA

Channel:

all the knowledge of the universe PRINCIPIA

Subscribers:

1,880

Published on January 19, 2022 7:12:51 PM ● Video Link: https://www.youtube.com/watch?v=SbtSvzCqZPc

Duration: 4:54

29 views

0

FASTA, by Wikipedia https://en.wikipedia.org/wiki?curid=1009996 / CC BY SA 3.0

#Computational_phylogenetics
#Bioinformatics_software
FASTA is a DNA and protein sequence alignment software package first described by David J. Lipman and William R. Pearson in 1985.
Its legacy is the FASTA format which is now ubiquitous in bioinformatics.
The original FASTP program was designed for protein sequence similarity searching.
Because of the exponentially expanding genetic information and the limited speed and memory of computers in the 1980s heuristic methods were introduced aligning a query sequence to entire data-bases.
FASTA, published in 1987, added the ability to do DNA:DNA searches, translated protein:DNA searches, and also provided a more sophisticated shuffling program for evaluating statistical significance.
There are several programs in this package that allow the alignment of protein sequences and DNA sequences.
Nowadays, increased computer performance makes it possible to perform searches for local alignment detection in a database using the Smith–Waterman algorithm.
FASTA is pronounced "fast A", and stands for "FAST-All", because it works with any alphabet, an extension of the original "FAST-P" （protein） and "FAST-N" （nucleotide） alignment tools.
Mappers timeline （since 2001）.
DNA mappers are plotted in blue, RNA mappers in red, miRNA mappers in green and bisulphite mappers in purple.
Grey dotted lines connect related mappers （extensions or new versions）.
The timeline only includes mappers with peer-reviewed publications, and the date corresponds to the earliest date of publication （e.g.
advanced publication date as opposed to the date of publication） The current FASTA package contains programs for protein:protein,
DNA:DNA, protein:translated DNA （with frameshifts）, and ordered or unordered peptide searches.
Recent versions of the FASTA package include special translated search algorithms that correctly handle frameshift errors （which six-frame-translated search...