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تعداد نتایج: 274 فیلتر نتایج به سال:
We present algorithms for the exact computation of the probability that a random string of a certain length matches a given regular expression. These algorithms can be used to determine statistical significance in a variety of pattern searches such as motif searches and gene-finding. This work improves upon work of Kleffe and Langebacker (Kleffe & Langbecker 1990) and of Sewell and Durbin (Sewe...
Human genes are often interrupted by non-coding, intragenic sequences called introns. Hence, the gene sequence is divided into exons (coding segments) and introns (non-coding segments). Consequently, a majority of them are multi exon genes (MEG). However, a considerable amount of single exon genes (SEG) are present in the human genome (approximately 12%). This amount is sizeable and it is impor...
In biology, the notion of degenerate pattern plays a central role for describing various phenomena. For example, protein active site patterns, like those contained in the PROSITE database, e.g., [FY ]DPC[LIM ][ASG]C[ASG], are, in general, represented by degenerate patterns with character classes. Researchers have developed several approaches over the years to discover degenerate patterns. Altho...
The purpose of this research is to search for motifs directly at binding and catalytic sites called reactive motifs, and then to predict enzyme functions from the discovered reactive motifs. The main challenge is that the data of binding, or catalytic sites is only available in the range 3.34% of all enzymes, and many of each data provides only one sequence record. The other challenge is the co...
The Blocks Database WWW (http://blocks.fhcrc.org ) and Email ([email protected] ) servers provide tools to search DNA and protein queries against the Blocks+ Database of multiple alignments, which represent conserved protein regions. Blocks+ nearly doubles the number of protein families included in the database by adding families from the Pfam-A, ProDom and Domo databases to those from PR...
This paper concerns the use of an object-oriented database for the analysis of protein sequences. We describe proteins either by bibliographic information or by prediction function such as Prosite patterns [2, 5]. We propose to use concept lattices|a tool used in information retrieval to build thesauruses|to classify protein sequences. This classi cation of proteins may help nding sequence alig...
We consider the problem of finding a set of patterns that best characterizes a set of strings. To this end, Arimura et. al. [3] considered the use of minimal multiple generalizations (mmg) for such characterizations. Given any sample set, the mmgs are, roughly speaking, the most (syntactically) specific set of languages containing the sample within a given class of languages. Takae et. al. [17]...
ProSAT (for Protein Structure Annotation Tool) is a tool to facilitate interactive visualization of non-structure-based functional annotations in protein 3D structures. It performs automated mapping of the functional annotations onto the protein structure and allows functional sites to be readily identified upon visualization. The current version of ProSAT can be applied to large datasets of pr...
We present a machine learning method to discriminate between cysteines involved in ligand binding and cysteines forming disulfide bridges. Our method uses a window of multiple alignment profiles to represent each instance and support vector machines with a polynomial kernel as the learning algorithm. We also report results obtained with two new kernel functions based on similarity matrices. Exp...
The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) was created in 1998 as an institution to foster excellence in bioinformatics. It is renowned worldwide for its databases and software tools, such as UniProtKB/Swiss-Prot, PROSITE, SWISS-MODEL, STRING, etc, that are all accessible on ExPASy.org, SIB's Bioinformatics Resource Portal. This article provides an overview of the scientific and...
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