We present further improvements on the computer system SMART (sequence motif analysis and retrieval tool) that assists biological interpretation of sequence data by searching sequence motifs in a query sequence and annotating functional features associated with the motifs found. The new version of the system fully utilizes the network communication based on a client-server model so that users r...

O-GLYCBASE is an updated database of information on glycoproteins and their O-linked glycosylation sites. Entries are compiled and revised from the literature, and from the SWISS-PROT database. Entries include information about species, sequence, glycosylation sites and glycan type. O-GLYCBASE is now fully cross-referenced to the SWISS-PROT, PIR, PROSITE, PDB, EMBL, HSSP, LISTA and MIM database...

Influenza A viruses of subtype H9N2 are wide spread among poultry and other mammalian species. Crossing the species barrier from poultry to human occurred in recent years creating a pandemic of H9N2 virus. It is known that the pathogenicity of H9N2 is lower than H5N1. Nonetheless, it is important to establish the molecular functions of H9N2 viral proteins. We studied mutations in the polymerase...

Bioinformatics has become indispensable to all fields in the life sciences. Its importance and impact to both theoretical and applied biology cannot be overestimated. The rapid progress of genome projects has brought a vast accumulation of molecular biological information in the past decade. Millions of nucleic acid sequences with billions of bases have been deposited in EMBL, GenBank and DDBJ....

MOTIVATION When evaluating the results of a sequence similarity search, there are many situations where it can be useful to determine whether sequences appearing in the results share some distinguishing characteristic. Such dependencies between database entries are often not readily identifiable, but can yield important new insights into the biological function of a gene or protein. RESULTS W...

PEP is a database of Predictions for Entire Proteomes. The database contains summaries of analyses of protein sequences from a range of organisms representing all three major kingdoms of life: eukaryotes, prokaryotes and archaea. All proteins publicly available for organisms were aligned against SWISS-PROT, TrEMBL and PDB. Additionally, the following annotations are provided: secondary structur...

Pattern discovery is limited to position-specific characterizations like Prosite’s patterns or profile-HMMs which are unable to handle, for instance, dependencies between amino acids distant in the sequence of a protein, but close in its three-dimensional structure. To overcome these limitations, we propose to learn automata on proteins. Inspired by grammatical inference and multiple alignment ...

Understanding the function of proteins continues to be a fundamental problem of biology[7]. Functional annotation of proteins through biological experimentation, however, is time-consuming and expensive. Many computational methods for prediction of protein function have been developed. Some tools, such as PSI-BLAST[2], EMATRIX[13], and PROSITE[6], use sequence similarity to help predict functio...

The iProClass database is an integrated resource that provides comprehensive family relationships and structural and functional features of proteins, with rich links to various databases. It is extended from ProClass, a protein family database that integrates PIR superfamilies and PROSITE motifs. The iProClass currently consists of more than 200,000 non-redundant PIR and SWISS-PROT proteins org...

Protein motifs, which are specific regions and conserved regions, are found by comparing multiple protein sequences. These conserved regions in general play an important role in protein functions and protein folds, for example, for their binding properties or enzymatic activities. The aim here is to find the existence correlations of protein motifs. The knowledge of protein motif/domain sharing...