Exact Transcriptome Reconstruction from Short Sequence Reads
作者： Vincent Lacroix , Michael Sammeth , Roderic Guigo , Anne Bergeron
DOI: 10.1007/978-3-540-87361-7_5
关键词: Gene 、 RNA 、 Set (abstract data type) 、 Data mining 、 Reconstruction problem 、 Sequence 、 Complement (set theory) 、 Transcriptome 、 Biology 、 Computational biology 、 Large set (Ramsey theory)
摘要: In this paper we address the problem of characterizing RNA complement a given cell type, that is, set species and their relative copy number, from large short sequence reads which have been randomly sampled cell's sequences through sequencing experiment. We refer to as transcriptome reconstruction problem, specifically investigate, both theoretically practically, conditions under can be solved. demonstrate that, even assumption exact information, neither single read nor paired-end guarantee has unique solution. However, by investigating behavior best annotated human gene set, also show in practice, --- but not may sufficient solve vast majority transcript variants abundances. finally when assume existing are known, effectively used infer variant
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