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Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in <Emphasis Type="Italic">Drosophila melanogaster</Emphasis> and <Emphasis Type="Italic">Drosophila pseudoobscura</Emphasis>
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Berman BP Pfeiffer BD Laverty TR Salzberg SL Rubin GM Eisen MB Celniker SE 《Genome biology》2004,5(9):R61
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Identification of sparsely distributed clusters of cis-regulatory elements in sets of co-expressed genes 总被引:4,自引:0,他引:4
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Kreiman G 《Nucleic acids research》2004,32(9):2889-2900
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MicroRNA identification based on sequence and structure alignment 总被引:20,自引:0,他引:20
MOTIVATION: MicroRNAs (miRNA) are approximately 22 nt long non-coding RNAs that are derived from larger hairpin RNA precursors and play important regulatory roles in both animals and plants. The short length of the miRNA sequences and relatively low conservation of pre-miRNA sequences restrict the conventional sequence-alignment-based methods to finding only relatively close homologs. On the other hand, it has been reported that miRNA genes are more conserved in the secondary structure rather than in primary sequences. Therefore, secondary structural features should be more fully exploited in the homologue search for new miRNA genes. RESULTS: In this paper, we present a novel genome-wide computational approach to detect miRNAs in animals based on both sequence and structure alignment. Experiments show this approach has higher sensitivity and comparable specificity than other reported homologue searching methods. We applied this method on Anopheles gambiae and detected 59 new miRNA genes. AVAILABILITY: This program is available at http://bioinfo.au.tsinghua.edu.cn/miralign. SUPPLEMENTARY INFORMATION: Supplementary information is available at http://bioinfo.au.tsinghua.edu.cn/miralign/supplementary.htm. 相似文献
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Finding motifs in the twilight zone 总被引:8,自引:0,他引:8