Permutation Pattern Discovery in Biosequences
نویسندگان
چکیده
منابع مشابه
Permutation Pattern Discovery in Biosequences
Functionally related genes often appear in each other's neighborhood on the genome; however, the order of the genes may not be the same. These groups or clusters of genes may have an ancient evolutionary origin or may signify some other critical phenomenon and may also aid in function prediction of genes. Such gene clusters also aid toward solving the problem of local alignment of genes. Simila...
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In this thesis we have developed novel methods for analyzing biological data, the primary sequences of the DNA and proteins, the microarray based gene expression data, and other functional genomics data. The main contribution is the development of the pattern discovery algorithm SPEXS, accompanied by several practical applications for analyzing real biological problems. For performing these bio...
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Protein, RNA and DNA are made up of sequences of amino acids/nucleotides, which interact among themselves via binding. For example, (1) protein-DNA binding regulates gene transcription [1]; and (2) Protein-protein binding plays important roles in cell cycle control and signal transduction [2].The binding is maintained by either the direct participation or assistance of conserved short segments ...
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In the last years, the information stored in biological data-sets grew up exponentially, and new methods and tools have been proposed to interpret and retrieve useful information from such data. Most biological data-sets contain biological sequences (e.g., DNA and protein sequences). Thus, it is much significant to have techniques available capable of mining patterns from such sequences to disc...
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We have extended the pattern language used in PROSITE to enable it to describe dependencies between amino acid residues. We have developed a minimum description length principle based tness measure evaluating the signiicance of such patterns in relation to a set of sequences, and an algorithm automatically nding signiicant patterns in unaligned sequences. Computing experiments are reported show...
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ژورنال
عنوان ژورنال: Journal of Computational Biology
سال: 2004
ISSN: 1066-5277,1557-8666
DOI: 10.1089/cmb.2004.11.1050