SABmark--a benchmark for sequence alignment that covers the entire known fold space

Bioinformatics
Ivo Van WalleLode Wyns

Abstract

The Sequence Alignment Benchmark (SABmark) provides sets of multiple alignment problems derived from the SCOP classification. These sets, Twilight Zone and Superfamilies, both cover the entire known fold space using sequences with very low to low, and low to intermediate similarity, respectively. In addition, each set has an alternate version in which unalignable but apparently similar sequences are added to each problem.

References

Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Oct 31, 1998·Protein Engineering·I N Shindyalov, P E Bourne
Oct 14, 2003·BMC Bioinformatics·G P S RaghavaGeoffrey J Barton
Dec 19, 2003·Nucleic Acids Research·John-Marc ChandoniaSteven E Brenner
Feb 14, 2004·Bioinformatics·Ivo Van WalleLode Wyns

❮ Previous
Next ❯

Citations

Jun 21, 2005·Current Opinion in Structural Biology·Iain M WallaceDesmond G Higgins
Mar 16, 2013·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·John Kececioglu, Dan DeBlasio
Aug 12, 2006·Omics : a Journal of Integrative Biology·Jim Leebens-MackChristian Zmasek
Jan 24, 2007·Bioinformatics·Ariel S Schwartz, Lior Pachter
Mar 3, 2007·Bioinformatics·Jason S Papadopoulos, Richa Agarwala
May 19, 2007·Bioinformatics·James A R Dalton, Richard M Jackson
Feb 7, 2008·Bioinformatics·Michael StoutNatalio Krasnogor
Aug 6, 2008·Bioinformatics·Virpi AholaEsa Uusipaikka
May 28, 2009·Bioinformatics·Jessica H Fong, Aron Marchler-Bauer
Aug 4, 2009·Bioinformatics·Carsten Kemena, Cedric Notredame
Oct 15, 2011·Bioinformatics·Xugang YeStephen F Altschul
Aug 5, 2009·Molecular Biology and Evolution·Cory L StropeEtsuko N Moriyama
Dec 20, 2005·Nucleic Acids Research·Timo Lassmann, Erik L L Sonnhammer
Dec 5, 2006·Nucleic Acids Research·Paolo SonegoSándor Pongor
Apr 25, 2007·Nucleic Acids Research·Jimin PeiNick V Grishin
Feb 22, 2008·Nucleic Acids Research·Jimin PeiNick V Grishin
May 27, 2008·Nucleic Acids Research·Jimin PeiNick V Grishin
Jan 6, 2010·Nucleic Acids Research·Robert C Edgar
Apr 24, 2010·Nucleic Acids Research·Sayed Mohammad Ebrahim Sahraeian, Byung-Jun Yoon
Jul 20, 2010·Nucleic Acids Research·Mohamed Radhouene AnibaJulie D Thompson
Apr 26, 2011·Nucleic Acids Research·Sayed Mohammad Ebrahim Sahraeian, Byung-Jun Yoon
Apr 27, 2013·Nucleic Acids Research·Layal Al AitBurkhard Morgenstern
Dec 15, 2010·Journal of Bioinformatics and Computational Biology·Tsan-Huang ShihHao-Teng Chang
Jan 28, 2010·BMC Bioinformatics·Jaebum Kim, Saurabh Sinha
Feb 4, 2010·BMC Bioinformatics·Ivaylo IlinkinRavi Janardan
May 24, 2011·BMC Bioinformatics·Catherine L AndersonEtsuko N Moriyama
May 23, 2012·BMC Bioinformatics·Paul Shealy, Homayoun Valafar
May 1, 2012·BMC Bioinformatics·Ilya Plyusnin, Liisa Holm
Jun 30, 2005·BMC Bioinformatics·Wouter Boomsma, Thomas Hamelryck
Mar 24, 2005·BMC Bioinformatics·Amarendran R SubramanianBurkhard Morgenstern
Oct 26, 2006·BMC Bioinformatics·Paulo A S NuinElisabeth R M Tillier
Sep 22, 2007·BMC Bioinformatics·Changhoon Kim, Byungkook Lee
Jul 13, 2007·BMC Bioinformatics·Timo Lassmann, Erik Ll Sonnhammer
Apr 29, 2008·BMC Bioinformatics·Emmanuel PerrodouJulie D Thompson
Dec 25, 2008·BMC Bioinformatics·Walter PirovanoJaap Heringa

❮ 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.