BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs
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چکیده
منابع مشابه
BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs
SUMMARY BAliBASE is a database of manually refined multiple sequence alignments categorized by core blocks of conservation sequence length, similarity, and the presence of insertions and N/C-terminal extensions. AVAILABILITY From http://www-igbmc. u-strasbg.fr/BioInfo/BAliBASE/index.html
متن کاملBAliBASE 3.0: latest developments of the multiple sequence alignment benchmark.
Multiple sequence alignment is one of the cornerstones of modern molecular biology. It is used to identify conserved motifs, to determine protein domains, in 2D/3D structure prediction by homology and in evolutionary studies. Recently, high-throughput technologies such as genome sequencing and structural proteomics have lead to an explosion in the amount of sequence and structure information av...
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BAliBASE is specifically designed to serve as an evaluation resource to address all the problems encountered when aligning complete sequences. The database contains high quality, manually constructed multiple sequence alignments together with detailed annotations. The alignments are all based on three-dimensional structural superpositions, with the exception of the transmembrane sequences. The ...
متن کاملSome remarks on evaluating the quality of the multiple sequence alignment based on the BAliBASE benchmark
BAliBASE is one of the most widely used benchmarks for multiple sequence alignment programs. The accuracy of alignment methods is measured by bali score—an application provided together with the database. The standard accuracy measures are the Sum of Pairs (SP) and the Total Column (TC). We have found that, for non-core block columns, results calculated by bali score are different from those ob...
متن کاملA benchmark of multiple sequence alignment programs upon structural RNAs
To date, few attempts have been made to benchmark the alignment algorithms upon nucleic acid sequences. Frequently, sophisticated PAM or BLOSUM like models are used to align proteins, yet equivalents are not considered for nucleic acids; instead, rather ad hoc models are generally favoured. Here, we systematically test the performance of existing alignment algorithms on structural RNAs. This wo...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 1999
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/15.1.87