This paper integrates the signal, context and structure features for genome-wide promoter recognition, which is critical in many DNA sequence analysis tasks. First, CpG islands ar...
Background: Searching for approximate patterns in large promoter sequences frequently produces an exceedingly high numbers of results. Our aim was to exploit biological knowledge ...
Stefania Bortoluzzi, Alessandro Coppe, Andrea Biso...
ppdb (http://www.ppdb.gene.nagoya-u.ac.jp) is a plant promoter database that provides promoter annotation of Arabidopsis and rice. The database contains information on promoter st...
: The standard practice in the analysis of promoters is to select promoter regions of convenient length. This may lead to false results when searching for Transcription Factor Bind...
Background: The analysis of the promoter sequence of genes with similar expression patterns is a basic tool to annotate common regulatory elements. Multiple sequence alignments ar...
Background: The use of global gene expression profiling to identify sets of genes with similar expression patterns is rapidly becoming a widespread approach for understanding biol...
Background: The discovery of cis-regulatory motifs still remains a challenging task even though the number of sequenced genomes is constantly growing. Computational analyses using...
Background: In our previous studies, we found that the sites in prokaryotic genomes which are most susceptible to duplex destabilization under the negative superhelical stresses t...
Background: Eukaryotic promoter prediction using computational analysis techniques is one of the most difficult jobs in computational genomics that is essential for constructing a...
Background: Promoter region plays an important role in determining where the transcription of a particular gene should be initiated. Computational prediction of eukaryotic Pol II ...
Jian-Yi Yang, Yu Zhou, Zu-Guo Yu, Vo Anh, Li-Qian ...