منابع مشابه
Regmex, Motif analysis in ranked lists of sequences
Motif analysis has long been an important method to characterize biological functionality and the current growth of sequencing-based genomics experiments further extends its potential. These diverse experiments often generate sequence lists ranked by some functional property. There is therefore a growing need for motif analysis methods that can exploit this coupled data structure and be tailore...
متن کاملEfficient motif search in ranked lists and applications to variable gap motifs
Sequence elements, at all levels-DNA, RNA and protein, play a central role in mediating molecular recognition and thereby molecular regulation and signaling. Studies that focus on -measuring and investigating sequence-based recognition make use of statistical and computational tools, including approaches to searching sequence motifs. State-of-the-art motif searching tools are limited in their c...
متن کاملStatistical Assessment of Enrichment in Ranked Lists - Algorithms and Applications in Motif Search
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متن کاملSupplemental Material for Regmex , Motif discovery in ranked lists of sequences
Figure S1: Regmex p-value output for different scenarios of sequence lengths, number of sequences and motif enrichements. (A) Random sequences (n=100) of length 100 nucleotides with a number of 7-mer motif (AATGCCC) inserted among the leading 30 sequences as indicated along the x-axis. (B) Random sequences (n=10,000) of length 100 nucleotides with a number of 7-mer motif (AATGCCC) inserted amon...
متن کاملMINER: software for phylogenetic motif identification
MINER is web-based software for phylogenetic motif (PM) identification. PMs are sequence regions (fragments) that conserve the overall familial phylogeny. PMs have been shown to correspond to a wide variety of catalytic regions, substrate-binding sites and protein interfaces, making them ideal functional site predictions. The MINER output provides an intuitive interface for interactive PM seque...
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ژورنال
عنوان ژورنال: Genome Biology
سال: 2010
ISSN: 1465-6906
DOI: 10.1186/gb-2010-11-2-r19