NDLI: Improved tools for biological sequence comparison.

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Improved tools for biological sequence comparison.

Content Provider	Semantic Scholar
Author	Pearson, William R. Lipman, David J.
Copyright Year	1988
Abstract	We have developed three computer programs for comparisons of protein and DNA sequences. They can be used to search sequence data bases, evaluate similarity scores, and identify periodic structures based on local sequence similarity. The FASTA program is a more sensitive derivative of the FASTP program, which can be used to search protein or DNA sequence data bases and can compare a protein sequence to a DNA sequence data base by translating the DNA data base as it is searched. FASTA includes an additional step in the calculation of the initial pairwise similarity score that allows multiple regions of similarity to be joined to increase the score of related sequences. The RDF2 program can be used to evaluate the significance of similarity scores using a shuffling method that preserves local sequence composition. The LFASTA program can display all the regions of local similarity between two sequences with scores greater than a threshold, using the same scoring parameters and a similar alignment algorithm; these local similarities can be displayed as a "graphic matrix" plot or as individual alignments. In addition, these programs have been generalized to allow comparison of DNA or protein sequences based on a variety of alternative scoring matrices.
File Format	PDF HTM / HTML
DOI	10.1073/pnas.85.8.2444
PubMed reference number	3162770
Journal	Medline
Volume Number	85
Issue Number	8
Alternate Webpage(s)	http://www.cs.nyu.edu/courses/spring08/G22.2520-001/biogenomes_docs/lec2-2444.pdf
Alternate Webpage(s)	https://gi.cebitec.uni-bielefeld.de/_media/teaching/2010summer/529fasta.pdf
Alternate Webpage(s)	https://doi.org/10.1073/pnas.85.8.2444
Journal	Proceedings of the National Academy of Sciences of the United States of America
Language	English
Access Restriction	Open
Content Type	Text
Resource Type	Article

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