BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations

BAliBASE is specifically designed to serve as an evaluation resource to add ress all the problems encountered when aligning complete sequences, The dat abase contains high quality, manually constructed multiple sequence alignme nts together with detailed annotations. The alignments are all based on thr ee-dimensional structural superpositions, with the exception of the transme mbrane sequences. The first release provided sets of reference alignments d ealing with the problems of high variability, unequal repartition and large NIC-terminal extensions and internal insertions. Here we describe version 2.0 of the database, which incorporates three new reference sets of alignme nts containing structural repeats, transmembrane sequences and circular per mutations to evaluate the accuracy of detection/prediction and alignment of these complex sequences. BAliBASE can be viewed at the web site http://www -igbmc.u-strasbg.fr/ BioInfo/BAliBASE2/index.html or can be downloaded from ftp://ftp-igbmc.u-strasbg.fr/pub/BAIiBASE2/.