Reconstruction of genuine pair-wise sequence alignment

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
Valery O PolyanovskyVladimir G Tumanyan

Abstract

In many applications, the algorithmically obtained alignment ideally should restore the "golden standard" (GS) alignment, which superimposes positions originating from the same position of the common ancestor of the compared sequences. The average similarity between the algorithmically obtained and GS alignments ("the quality") is an important characteristic of an alignment algorithm. We proposed to determine the quality of an algorithm, using sequences that were artificially generated in accordance with an appropriate evolution model; the approach was applied to the global version of the Smith-Waterman algorithm (SWA). The quality of SWA is between 97% (for a PAM distance of 60) and 70% (for a PAM distance of 300). The percentage of identical aligned residues is the same for algorithmic and GS alignments. The total length of indels in algorithmic alignments is less than in the GS-mainly due to a substantial decrease in the number of indels in algorithmic alignments.

References

Jul 1, 1990·Protein Engineering·M Vingron, P Argos
Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Mar 22, 1985·Science·D J Lipman, W R Pearson
Mar 1, 1970·Journal of Molecular Biology·S B Needleman, C D Wunsch
Mar 25, 1981·Journal of Molecular Biology·T F Smith, M S Waterman
Feb 1, 1996·Protein Engineering·H T Mevissen, M Vingron
Jun 2, 1998·Bioinformatics·J StoyeF Meyer
Mar 29, 2000·Journal of Molecular Biology·F S DominguesM J Sippl
Jun 21, 2002·Bioinformatics·Maximilian Schlosshauer, Mattias Ohlsson
Nov 9, 2002·Bioinformatics·J T Reese, W R Pearson
Jan 22, 2005·Nature·I King JordanShamil Sunyaev
Jul 29, 2005·Molecular Biology and Evolution·Volker HollichErik L L Sonnhammer

❮ Previous
Next ❯

Citations

May 11, 2011·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Lu MengMichael S Waterman
Oct 29, 2011·Algorithms for Molecular Biology : AMB·Valery O PolyanovskyVladimir G Tumanyan

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

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

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.

Microbicide

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.