To take into account database redundancy, we grouped proteins with the same set or subset of unique peptides and identified a "protein group leader", which usually was the protein with the largest number of peptides.
We further analyzed only those cases in which six or more copies of a given IS family were found per chromosome and, to avoid database redundancy, in only one strain for each bacterial species (supplementary table S4, Supplementary Material online).
Through this method they were able to test and identify several SNPs without compromising database size, redundancy and reliability of the results.
In the database, the redundancy due to varying fatty acid composition for the same molecular weight can be represented using the common notation showing total number of carbons and double bonds.
Interestingly, the partial sequence of the element FL4 (GenBank ID GU929874) was found to have 365 hits, representing a copy number estimate of ~516 in the genome when taking into consideration the genome size, size of the BES database and redundancy of the library.
With the growing use of XML as a format for the permanent storage of data, the study of functional dependencies in XML (XFDs) is of fundamental importance in a number of areas such as understanding how to effectively design XML databases without redundancy or update problems, and data integration.
The normalized syntax will allow exchange of data with other databases, reduce redundancies, and provides a framework for future annotations.
Partial, putative, synthetic construct, predicted, not experimental, hypothetical protein, r-RNA, t-RNA, ribosomal and mitochondrial genes were eliminated and then the cleanup program [ 31] was applied for ridding nucleotide sequence databases of redundancies.
The popular pruning techniques include chi-square testing, database coverage, rule redundancy, conflicting rules and pessimistic error estimation etc [13].
Current systems biology experts are in the quest of cleaning and populating available database with minimal redundancy in the hope of exhaustive coverage of cellular biochemical reactions.
This assignment is implemented in an automated script, thus preventing that one protein from the same organism may occur in duplicate within the database and avoiding redundancy even if it may occur in GenBank.
