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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...
Biomedical named entity recognition, an important step, makes preparation for extracting information from biomedical textual resources. This paper presents a hybrid approach to recognize biomedical entity, which includes POS (Part-of-Speech) tagging, rules-based and dictionary-based approach using biomedical ontology. Experiment results show our approach can find untagged biomedical entity name in...
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...
Although the observations concerning the factors which influence the siRNA efficacy give clues to the mechanism of RNAi, the quantitative prediction of the siRNA efficacy is still a challenge task. In this paper, we introduced a novel non-linear regression method: random forest regression (RFR), to quantitatively estimate siRNAs efficacy values. Compared with an alternative machine learning regression...
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