HIGEDA: a hierarchical gene-set genetics based algorithm for finding subtle motifs in biological sequences
نویسندگان
چکیده
منابع مشابه
HIGEDA: a hierarchical gene-set genetics based algorithm for finding subtle motifs in biological sequences
MOTIVATION Identification of motifs in biological sequences is a challenging problem because such motifs are often short, degenerate, and may contain gaps. Most algorithms that have been developed for motif-finding use the expectation-maximization (EM) algorithm iteratively. Although EM algorithms can converge quickly, they depend strongly on initialization parameters and can converge to local ...
متن کاملFinding subtle motifs with variable gaps in unaligned DNA sequences
Biologists have determined that the control and regulation of gene expression is primarily determined by relatively short sequences in the region surrounding a gene. These sequences vary in length, position, redundancy, orientation, and bases. Finding these short sequences is a fundamental problem in molecular biology with important applications. Though there exist many different approaches to ...
متن کاملA Hierarchical Gene-Set Genetic Algorithm
In this paper, gene sets, instead of individual genes, are used in the genetic process to speed up convergence. A gene-set mutation operator is proposed, which can make several neighboring genes to simultaneously mutate. A gene-set crossover operator is also designed to choose the crossover points at the boundary of gene sets. The proposed gene-set mutation and crossover operators will cause a ...
متن کاملqPMS7: A Fast Algorithm for Finding (ℓ, d)-Motifs in DNA and Protein Sequences
Detection of rare events happening in a set of DNA/protein sequences could lead to new biological discoveries. One kind of such rare events is the presence of patterns called motifs in DNA/protein sequences. Finding motifs is a challenging problem since the general version of motif search has been proven to be intractable. Motifs discovery is an important problem in biology. For example, it is ...
متن کاملFinding Weak Motifs in DNA Sequences
Recognition of regulatory sites in unaligned DNA sequences is an old and well-studied problem in computational molecular biology. Recently, large-scale expression studies and comparative genomics brought this problem into a spotlight by generating a large number of samples with unknown regulatory signals. Here we develop algorithms for recognition of signals in corrupted samples (where only a f...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Bioinformatics
سال: 2009
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/btp676