000114898 001__ 114898
000114898 005__ 20181203021032.0
000114898 0247_ $$2doi$$a10.1093/bioinformatics/btg1029
000114898 037__ $$aARTICLE
000114898 245__ $$aAPDB: a novel measure for benchmarking sequence alignment methods without reference alignments
000114898 269__ $$a2003
000114898 260__ $$c2003
000114898 336__ $$aJournal Articles
000114898 500__ $$aDepartment of Biochemistry, University College, Cork, Ireland.
000114898 520__ $$aMOTIVATION: We describe APDB, a novel measure for evaluating the quality of a protein sequence alignment, given two or more PDB structures. This evaluation does not require a reference alignment or a structure superposition. APDB is designed to efficiently and objectively benchmark multiple sequence alignment methods. RESULTS: Using existing collections of reference multiple sequence alignments and existing alignment methods, we show that APDB gives results that are consistent with those obtained using conventional evaluations. We also show that APDB is suitable for evaluating sequence alignments that are structurally equivalent. We conclude that APDB provides an alternative to more conventional methods used for benchmarking sequence alignment packages.
000114898 700__ $$aO'Sullivan, O.
000114898 700__ $$aZehnder, M.
000114898 700__ $$aHiggins, D.
000114898 700__ $$0244404$$g113607$$aBucher, P.
000114898 700__ $$aGrosdidier, A.
000114898 700__ $$aNotredame, C.
000114898 773__ $$j19 Suppl 1$$tBioinformatics$$qi215-21
000114898 909C0 $$xU11780$$0252244$$pGR-BUCHER
000114898 909CO $$pSV$$particle$$ooai:infoscience.tind.io:114898
000114898 937__ $$aGR-BUCHER-ARTICLE-2003-006
000114898 973__ $$rREVIEWED$$sPUBLISHED$$aOTHER
000114898 980__ $$aARTICLE