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MicroRNAs (miRNAs) are small noncoding RNAs which regulate gene expression. In this research, we used the Multiz alignments data of 44 Vertebrates to retrieve syntenic homolog sequences. And we identified 37 members of miR-1302 family among 71 potential homolog sequences. Then we analyzed the 37 homologs of hsa-mir-1302s by RepeatMasker and found all of these sequences are derived from MER53 elements...
Many high-throughput DNA sequencing methods provide very short reads, typically of a few tens of base pairs. New algorithms and softwares are needed to analysis those short reads effectively. There are some software tools for aligning short reads to a reference genome. Here we introduce a new method, Umap, to align theses short reads faster and more exact. Applying Umap to simulated very short reads...
Protein-DNA interactions are vitally important in a wide range of biological processes such as gene regulation and DNA replication and repair. We predict DNA-binding residues in proteins from amino acid sequences by support vector machine (SVM) with a novel hybrid feature which incorporates evolutionary information of amino acid sequences and four physical-chemical properties, including the side chain...
Base-base correlation (BBC), as a novel sequence feature, reflects genome information structure. BBC has been applied to distinguish various functional regions of genomes. Meanwhile, as a genomic signature, BBC is used to compare sequences from different species. The database based on BBC feature has been constructed to search for similar sequences. It has been found that BBC carries a strong phylogenetic...
Hurst indexes of exon, intron and promoter sequences were studied based on Z-curve. For z variable of Z-curve, Hurst index distribution curves of the exons and introns had a great difference, and the distribution curve of the promoters overlapped with those of exons and introns. For other viable y and x of Z-curve, the exons, introns and promoters had a similar Hurst index distribution. It was also...
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