APDB: a novel measure for benchmarking sequence alignment methods without reference alignments

O. O'Sullivan; M. Zehnder; D. Higgins; P. Bucher; A. Grosdidier; C. Notredame
January 2009
Bioinformatics;Jan2009 Supplement, Vol. 19, p215
Academic Journal
Motivation: We describe APDB, a novel measure for evaluating the quality of a protein sequence alignment, given two or more PDB structures. This evaluation does not require a reference alignment or a structure superposition. APDB is designed to efficiently and objectively benchmark multiple sequence alignment methods. Results: Using existing collections of reference multiple sequence alignments and existing alignment methods, we show that APDB gives results that are consistent with those obtained using conventional evaluations. We also show that APDB is suitable for evaluating sequence alignments that are structurally equivalent. We conclude that APDB provides an alternative to more conventional methods used for benchmarking sequence alignment packages. Availability: APDB is implemented in C, its source code and its documentation are available for free on request from the authors. Contact: cedric.notredame@europe.com


Related Articles

  • Prediction of the translocon-mediated membrane insertion free energies of protein sequences. Yungki Park; Volkhard Helms // Bioinformatics;May2008, Vol. 24 Issue 10, p1271 

    Motivation: Helical membrane proteins (HMPs) play crucial roles in a variety of cellular processes. Unlike water-soluble proteins, HMPs need not only to fold but also get inserted into the membrane to be fully functional. This process of membrane insertion is mediated by the translocon complex....

  • Expression and Molecular Characterization of Spherical Particles Derived from the Genome of the Hyperthermophilic Euryarchaeote Pyrococcus furiosus. Namba, Kazunori; Hagiwara, Kyoji; Tanaka, Hideaki; Nakaishi, Yuichiro; Khoon Tee Chong; Yamashita, Eiki; Armah, George Enyimah; Ono, Yasuko; Ishino, Yoshizumi; Omura, Toshihiro; Tsukihara, Tomitake; Nakagawa, Atsushi // Journal of Biochemistry;Aug2005, Vol. 138 Issue 2, p193 

    Spherical particles (SPs) of approximately 30 nm in diameter were found in the hyperthermophilic archaeon Pyrococcus furiosus. The SPs contained no nucleic acid and were composed of a single 39-kDa protein. The amino acid sequences of the amino-terminal and internal fragments were identical to...

  • Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space. Yaniv Loewenstein; Elon Portugaly; Menachem Fromer; Michal Linial // Bioinformatics;Jul2008, Vol. 24 Issue 13, pi41 

    Motivation: UPGMA (average linking) is probably the most popular algorithm for hierarchical data clustering, especially in computational biology. However, UPGMA requires the entire dissimilarity matrix in memory. Due to this prohibitive requirement, UPGMA is not scalable to very large datasets....

  • MACHOS: Markov clusters of homologous subsequences. Simon Wong; Mark A. Ragan // Bioinformatics;Jul2008, Vol. 24 Issue 13, pi77 

    Motivation: The classification of proteins into homologous groups (families) allows their structure and function to be analysed and compared in an evolutionary context. The modular nature of eukaryotic proteins presents a considerable challenge to the delineation of families, as different local...

  • Protein structure alignment considering phenotypic plasticity. Gergely Csaba; Fabian Birzele; Ralf Zimmer // Bioinformatics;Aug2008, Vol. 24 Issue 16, pi98 

    Motivation: Protein structure comparison exhibits differences and similarities of proteins and protein families and may help to elucidate protein sequence and structure evolution. Despite many methods to score protein structure similarity with and without.exibility and to align proteins...

  • Protein coalitions in a core mammalian biochemical network linked by rapidly evolving proteins. Ainali, Chrysanthi; Simon, Michelle; Freilich, Shiri; Espinosa, Octavio; Hazelwood, Lee; Tsoka, Sophia; Ouzounis, Christos A.; Hancock, John M. // BMC Evolutionary Biology;2011, Vol. 11 Issue 1, p142 

    Background: Cellular ATP levels are generated by glucose-stimulated mitochondrial metabolism and determine metabolic responses, such as glucose-stimulated insulin secretion (GSIS) from the β-cells of pancreatic islets. We describe an analysis of the evolutionary processes affecting the core...

  • Solenoid and non-solenoid protein recognition using stationary wavelet packet transform. An Vo; Nha Nguyen; Heng Huang // Bioinformatics;Sep2010, Vol. 26 Issue 18, pi467 

    Motivation: Solenoid proteins are emerging as a protein class with properties intermediate between structured and intrinsically unstructured proteins. Containing repeating structural units, solenoid proteins are expected to share sequence similarities. However, in many cases, the sequence...

  • Computational structural and functional characterization of protein family: Key for the hidden mystery. Umang, Malhotra; Astha, Jaiswal; Aastha, Chhabra; Neha, Atale; Vibha, Rani // Journal of Pharmacy Research;2012, Vol. 5 Issue 7, p3643 

    With the accretion of raw biological data in the form of unannotated protein sequences, biologists are seeking solutions to unravel the functions of proteins which have not yet been characterized experimentally. The numerous bioinformatics tools available can be used to gain an insight into...

  • Expanding the Versatility of Phage Display I: Efficient Display of Peptide-Tags on Protein VII of the Filamentous Phage. Løset, Geir Åge; Bogen, Bjarne; Sandlie, Inger // PLoS ONE;2011, Vol. 6 Issue 2, p1 

    Background: Phage display is a platform for selection of specific binding molecules and this is a clear-cut motivation for increasing its performance. Polypeptides are normally displayed as fusions to the major coat protein VIII (pVIII), or the minor coat protein III (pIII). Display on other...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics