Summary: BAliBASE is a database of manually-refined multiple sequence alignments specifically
designed for the evaluation and comparison of multiple sequence alignment programs. The
alignments are categorised by sequence length, similarity, and presence of insertions and N/C-
terminal extensions. Core blocks are identified excluding non-superposable regions.
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Look at a list of all the alignments.
The alignment of protein sequences is a crucial tool in molecular biology and genome analysis. Historically, the quality of new alignment programs has been compared to previous methods using a small number of test cases selected by the program author (eg. Smith and Smith, 1992; Eddy, 1995; Morgenstern et al., 1996; Deperieux et al., 1997; Thompson et al., 1997). Recently, some comparisons have been done using a set of alignments selected from structural databases (Gotoh, 1996; Notredame et al., 1998). However, the databases currently available (Pascarella et al., 1996; Holm and Sander, 1998; Mizuguchi et al., 1998; Sowdhamini et al., 1998) assemble proteins into homologous families. The alignments are not structured and classified specifically for the systematic evaluation of multiple alignment programs.
A comprehensive evaluation and comparison of alignment programs requires a large number of accurate reference alignments which can be used as test cases. It has been shown (McClure et al., 1994) that the performance of alignment programs depends on the number of sequences, the degree of similarity between sequences and the number of insertions in the alignment. Other factors may also affect alignment quality such as the length of the sequences, the existence of large insertions and N/C-terminal extensions and over-representation of some members of the protein family. We have constructed BAliBASE (Benchmark Aligment dataBASE) containing high- quality, documented alignments to identify the strong and weak points of the numerous alignment programs now available.
A frequent problem encountered when using reference alignments has been the effect of ambiguous regions in the sequences which cannot be structurally superposed. Very distantly related sequences often have only short conserved motifs in long regions of low overall similarity. These regions can only be aligned arbitrarily in the reference and may lead to a bias in the comparison of programs. In BAliBASE, we have annotated the core blocks in the alignments that only include the regions that can be reliably aligned. The blocks exclude regions where there is a possibility of ambiguity in the alignment. This may be an important factor affecting the significance of statistical comparisons of alignment programs.
The sequences included in the database are selected from alignments in either the FSSP or HOMSTRAD structural databases, or from manually constructed structural alignments taken from the literature. When sufficient structures are not available, additional sequences are included from the HSSP database (Schneider et al., 1997). The VAST Web server (Madej, 1995) is used to confirm that the sequences in each alignment are structural neighbours and can be structurally superimposed. Functional sites are identified using the PDBsum database (Laskowski et al., 1997) and the alignments are manually verified and adjusted, in order to ensure that conserved residues are aligned as well as the secondary structure elements.
BAliBASE currently consists of 142 reference alignments, containing over 1000 sequences. Of the 200,000 residues in the database, 58% are defined within the core blocks. The remaining 42% are in ambiguous regions that cannot be reliably aligned. The alignments are divided into four hierarchical reference sets, reference 1 providing the basis for construction of the following sets. Each of the main sets may be further sub-divided into smaller groups, according to sequence length and percent similarity.
Reference 1 contains alignments of (less than 6) equi-distant sequences, ie. the percent identity between two sequences is within a specified range. All the sequences are of similar length, with no large insertions or extensions. Reference 2 aligns up to three "orphan" sequences (less than 25% identical) from reference 1 with a family of at least 15 closely related sequences. Reference 3 consists of up to 4 sub-groups, with less than 25% residue identity between sequences from different groups. The alignments are constructed by adding homologous family members to the more distantly related sequences in reference 1. Reference 4 is divided into two sub-categories containing alignments of up to 20 sequences including N/C-terminal extensions (up to 400 residues), and insertions (up to 100 residues).
The alignments are provided in either RSF format, or MSF format with an attached text file containing a list of the known secondary structure elements for each sequence. Each alignment is also associated with an annotation file containing a description of the alignment. The annotation is divided into 4 sections: (i) a general description of the alignment (ii) the sequence repartition showing sub-groups and orphans (iii) the major insertions (iv) the core blocks in the alignment.
In the future, new reference sections could be added to BaliBASE to include other criteria that affect the performance of alignment programs, particularly transmembrane proteins and other sequences showing a compositional bias.
A comparison of alignment programs (work in progress) suggests that not all of the alignment algorithms react in the same way to the problems presented in the BAliBASE alignments. The results of the study should allow users to select the most suitable program for a particular task depending on the set of sequences to be aligned, thus improving the accuracy of the automatic alignment and reducing the manual refinement required to obtain the final, optimal alignment.
If you have any problems/comments/questions, please e-mail Julie ThompsonWe would like to thank M. Bergdoll, L Moulinier and J-M Wurtz for allowing us to include their structural alignments in the database. We would also like to thank D. Moras and J-C. Thierry for their support during this work and F. Jeanmougin and T. Gibson for useful discussions. The work was supported by institute funds from INSERM, CNRS, H.U.S. and Bristol-MYERS SQUIBB.
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