MinSet: a general approach to derive maximally representative database subsets by using fragment dictionaries and its application to the SCOP database.
BACKGROUND
The size of current protein databases is a challenge for many Bioinformatics applications, both in terms of processing speed and information redundancy. It may be therefore desirable to efficiently reduce the database of interest to a maximally representative subset.


RESULTS
The MinSet method employs a combination of a Suffix Tree and a Genetic Algorithm for the generation, selection and assessment of database subsets. The approach is generally applicable to any type of string-encoded data, allowing for a drastic reduction of the database size whilst retaining most of the information contained in the original set. We demonstrate the performance of the method on a database of protein domain structures encoded as strings. We used the SCOP40 domain database by translating protein structures into character strings by means of a structural alphabet and by extracting optimized subsets according to an entropy score that is based on a constant-length fragment dictionary. Therefore, optimized subsets are maximally representative for the distribution and range of local structures. Subsets containing only 10% of the SCOP structure classes show a coverage of >90% for fragments of length 1-4.


BACKGROUND
http://mathbio.nimr.mrc.ac.uk/~jkleinj/MinSet.


BACKGROUND
Supplementary data are available at Bioinformatics online.
Pandini
Alessandro
A
Dipartimento di Scienze dell'Ambiente e del Territorio, Università degli Studi di Milano-Bicocca, Milano, Italy.
Bonati
Laura
L
Fraternali
Franca
F
Kleinjung
Jens
J
D000465:Algorithms; D044962:Data Compression / Q000379:methods*; D003628:Database Management Systems; D030562:Databases, Protein; D004015:Dictionaries, Chemical as Topic; D010446:Peptide Fragments / Q000737:chemistry / Q000145:classification; D011506:Proteins / Q000737:chemistry* / Q000145:classification*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
D010446:Peptide Fragments; D011506:Proteins