This paper focuses on the problem of distributed sequence prediction in a network of sparsely interconnected agents, where agents collaborate to achieve provably reasonable predictive performance. An expert assisted online learning algorithm in a distributed setup of the consensus+innovations form is proposed, in which the agents update their weights for the experts’ predictions by simultaneous...

Most organisms use different mechanisms of translation termination for the three types of stop codons, i.e. UAA, UAG, and UGA [1]. Using the GenBank database, we have conducted comprehensive computer analyses of translation termination sites in order to find the difference of consensus sequence patterns around each type of stop codons. We also systematically analyzed the preference of stop codo...

Single Nucleotide Polymorphisms (SNPs) in virtual expressed gene fragment alignments represent a potentially signi cant resource for both the detection of non-coding and coding, sequence variations. We have clustered and assembled 767 866 human ESTs into 76 131 alignments localised to speci c tissues [1]. In addition, we have clustered and aligned 300 000 consensus sequences and unclustered EST...

We address the problem of detecting consensus motifs, that occur with subtle variations, across multiple sequences. These are usually functional domains in DNA sequences such as transcriptional binding factors or other regulatory sites. The problem in its generality has been considered difficult and various benchmark data serve as the litmus test for different computational methods. We present ...

The TBestDB database contains approximately 370,000 clustered expressed sequence tag (EST) sequences from 49 organisms, covering a taxonomically broad range of poorly studied, mainly unicellular eukaryotes, and includes experimental information, consensus sequences, gene annotations and metabolic pathway predictions. Most of these ESTs have been generated by the Protist EST Program, a collabora...

Recently the gene responsible for Pendred syndrome (PDS) was isolated and several mutations in the PDS gene have been identified in Pendred patients. Here we report the occurrence of two diVerent PDS mutations in an extended inbred Turkish family. The majority of patients in this family are homozygous for a splice site mutation (1143-2A→G) aVecting the 3' splice site consensus sequence of intro...

Listeria monocytogenes can cause serious infection and recently, relapse of listeriosis has been reported in leukemia and colorectal cancer, and the patients with Klebsiella pneumoniae are at increased risk of colorectal cancer. Translation initiation codon recognition is basically mediated by Shine-Dalgarno (SD) and the anti-SD sequences at the small ribosomal RNA (ssu rRNA). In this research,...

Signal search analysis is a general method to discover and characterize sequence motifs that are positionally correlated with a functional site (e.g. a transcription or translation start site). The method has played an instrumental role in the analysis of eukaryotic promoter elements. The signal search analysis server provides access to four different computer programs as well as to a large num...

Cysteine-rich intestinal protein 1 (CRIP1) has been identified as a novel marker for early detection of cancers. Here we report on the use of phage display in combination with molecular modeling to identify a high-affinity ligand for CRIP1. Panning experiments using a circularized C7C phage library yielded several consensus sequences with modest binding affinities to purified CRIP1. Two sequenc...

MOTIVATION The expanding protein sequence and structure databases await methods allowing rapid similarity search. Geometric parameters-dihedral angle between two sequential peptide bond planes (V) and radius of curvature (R) as they appear in pentapeptide fragments in polypeptide chains-are proposed for use in evaluating structural similarity in proteins (VeaR). The parabolic (empirical) functi...