PROSITE is a compilation of sites and patterns found in protein sequences; it can be used as a method of determining the function of uncharacterized proteins translated from genomic or cDNA sequences. In some cases the sequence of an unknown protein is too distantly related to any protein of known structure to detect its resemblance by overall sequence alignment, but relationships can be reveal...

The baker’s yeast Saccharomyces cerevisiae was the first eukaryotic organism to have its complete genome sequence determined, revealing 30 distinct genes encoding ATP-binding cassette (ABC) proteins (Bauer et al., 1999; Decottignies and Goffeau, 1997; Taglicht and Michaelis, 1998). ABC proteins are ubiquitous and form one of the largest gene families known with more than 2000 distinct ABC genes...

Sequence signature databases such as PROSITE, which include amino acid segments that are indicative of a protein's function, are useful for protein annotation. Lamentably, the annotation is not always accurate. A signature may be falsely detected in a protein that does not carry out the associated function (false positive prediction, FP) or may be overlooked in a protein that does carry out the...

Reliable functional annotation of genomic data is the key-step in the discovery of novel enzymes. Intrinsic sequencing data quality problems of single amplified genomes (SAGs) and poor homology of novel extremophile's genomes pose significant challenges for the attribution of functions to the coding sequences identified. The anoxic deep-sea brine pools of the Red Sea are a promising source of n...

The baker’s yeast Saccharomyces cerevisiae was the first eukaryotic organism to have its complete genome sequence determined, revealing 30 distinct genes encoding ATP-binding cassette (ABC) proteins (Bauer et al., 1999; Decottignies and Goffeau, 1997; Taglicht and Michaelis, 1998). ABC proteins are ubiquitous and form one of the largest gene families known with more than 2000 distinct ABC genes...

Classi cation of cDNA/protein sequence data is necessary for analysis and further application of sequence data, i.e. understanding of pathway of proteins in a cell and signal transduction. Since rapid increase of the number of cDNA/protein sequences is expected, the procedure of the classi cation must be systematic and automated to avoid human eye inspection. In this study, the sequence data ar...

We define the best consensus motif (BCM) problem motivated by the problem of extracting motifs from nucleic acid and amino acid sequences. A type over an alphabet C is a family R of subsets of C*. A motif ;.r of type R is a string ;.r = 7~1 . ;.rn of motif components, each of which stands for an element in R. The BCM problem for R is, given a yes-no sample S = {(a('), @('I), . . . , (dm) , dm))...

Imposing constraints is an effective means to incorporate biological knowledge into alignment procedures. As in the PROSITE database, functional sites of proteins can be effectively described as regular expressions. In an alignment of protein sequences it is natural to expect that functional motifs should be aligned together. Due to this motivation, Arslan introduced the regular expression cons...

Classification of cDNA/protein sequence data is necessary for analysis and further application of sequence data, i.e. understanding of pathway of proteins in a cell and signal transduction. Since rapid increase of the number of cDNA/protein sequences is expected, the procedure of the classification must be systematic and automated to avoid human eye inspection. In this study, the sequence data ...

Automated methods of machine learning may prove to be useful in discovering biologically meaningful information hidden in the rapidly growing databases of DNA sequences and protein sequences. Genetic programming is an extension of the genetic algorithm in which a population of computer programs is bred, over a series of generations, in order to solve a problem. Genetic programming is capable of...