PMID: 3162770Apr 1, 1988Paper

Improved tools for biological sequence comparison

Proceedings of the National Academy of Sciences of the United States of America
W R Pearson, D J Lipman


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 alternativ...Continue Reading


Mar 22, 1985·Science·D J Lipman, W R Pearson
Mar 1, 1970·Journal of Molecular Biology·S B Needleman, C D Wunsch
Jan 11, 1982·Nucleic Acids Research·J P Dumas, J Ninio
Feb 1, 1983·Proceedings of the National Academy of Sciences of the United States of America·W J Wilbur, D J Lipman
Jan 11, 1984·Nucleic Acids Research·D J LipmanM S Waterman
Dec 1, 1981·Proceedings of the National Academy of Sciences of the United States of America·J V Maizel, R P Lenk
Mar 25, 1981·Journal of Molecular Biology·T F Smith, M S Waterman

❮ Previous
Next ❯


Nov 20, 1998·American Journal of Physical Anthropology·M UbaldiF Rollo
Jul 22, 1998·Proteins·J Wouters, G Baudoux
Oct 3, 1999·Cell Motility and the Cytoskeleton·A L BomanR A Kahn
Feb 1, 1996·Developmental Dynamics : an Official Publication of the American Association of Anatomists·K SalmivirtaP Ekblom
Sep 18, 1998·Molecular Reproduction and Development·X Zhu, R K Naz
Oct 15, 1998·Molecular Reproduction and Development·S D'Andréa, C La Bonnardière
Jan 1, 1996·Journal of Clinical Laboratory Analysis·M Mitsuhashi
Jun 22, 2000·American Journal of Physical Anthropology·R J CanoF Rollo
Jun 27, 2000·Journal of Molecular Recognition : JMR·S B NaglT F Smith
Nov 1, 2000·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·UNKNOWN CODATA Task Group on biological macromolecules and colleagues. Committee on Data for Science and Technology of the Internati
Mar 29, 2001·Electrophoresis·H E Kristoffersen, R Flengsrud
Mar 29, 2001·Electrophoresis·J T RegulaR Frank
Sep 1, 1993·Developmental Dynamics : an Official Publication of the American Association of Anatomists·T ShirasawaK Hirokawa
Jul 17, 2008·Comparative and Functional Genomics·A J PérezG Thode
Jul 17, 2008·Comparative and Functional Genomics·Keith FlanaganAnil Wipat
Jul 17, 2008·Comparative and Functional Genomics·Catarina MoitaPedro Fernandes
Jul 17, 2008·Comparative and Functional Genomics·K C WoodwarkS G Oliver
Jul 17, 2008·Comparative and Functional Genomics·V WoodB Barrell
Nov 1, 1993·Electrophoresis·P J WirthD C Parmelee

❮ Previous
Next ❯

Related Concepts

Trending Feeds


Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.


Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.


Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Journal of Molecular Biology
S F AltschulD J Lipman
Journal of Molecular Biology
T F Smith, M S Waterman
Proceedings of the National Academy of Sciences of the United States of America
F SangerA F Coulson
© 2022 Meta ULC. All rights reserved