Fast and Flexible Text Search Using Genomic Short-Read Mapping Model
نویسندگان
چکیده
منابع مشابه
X-MATE: a flexible system for mapping short read data
SUMMARY Accurate and complete mapping of short-read sequencing to a reference genome greatly enhances the discovery of biological results and improves statistical predictions. We recently presented RNA-MATE, a pipeline for the recursive mapping of RNA-Seq datasets. With the rapid increase in genome re-sequencing projects, progression of available mapping software and the evolution of file forma...
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Today, with rapid growth of the World Wide Web and creation of Internet sites and online text resources, text summarization issue is highly attended by various researchers. Extractive-based text summarization is an important summarization method which is included of selecting the top representative sentences from the input document. When, we are facing into large data volume documents, the extr...
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UNLABELLED We report on a major update (version 2) of the original SHort Read Mapping Program (SHRiMP). SHRiMP2 primarily targets mapping sensitivity, and is able to achieve high accuracy at a very reasonable speed. SHRiMP2 supports both letter space and color space (AB/SOLiD) reads, enables for direct alignment of paired reads and uses parallel computation to fully utilize multi-core architect...
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MOTIVATION Genome resequencing and short read mapping are two of the primary tools of genomics and are used for many important applications. The current state-of-the-art in mapping uses the quality values and mapping quality scores to evaluate the reliability of the mapping. These attributes, however, are assigned to individual reads and do not directly measure the problematic repeats across th...
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The author proposes a new data structure (TS{ le) in order to make a fast search for an arbitrary string in a large full text stored in secondary storage. The TS{ le stores the location of every string of length L (the level) in the text. Using this, we can e ciently search for, not only strings of length L but also those shorter than or longer than L. From an analysis of search cost, the numbe...
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ژورنال
عنوان ژورنال: ETRI Journal
سال: 2016
ISSN: 1225-6463
DOI: 10.4218/etrij.16.0115.0594