Mapping short reads to a genome without using hash look-up table algorithm and Burrows Wheeler Transformation

Chun Yuan Lin, Ming Yuan Huang, Chia Han Chu, Petrus Tang, Chuan Yi Tang

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

2 Scopus citations

Abstract

Many new sequencing techniques have been proposed in the last few years. A number of tools have been developed for mapping short reads to the genome. However, these tools used the hash look-up table algorithm for reads or for the genome. With more and more reads sequenced and the length of reads increases; these tools will require huge memory usage and may be not practical for biologists and applications. Recently, new tools were designed to overcome this problem by using Burrows Wheeler Transformation. In this paper, we propose a program, FRESCO, without using hash look-up table algorithm and Burrows Wheeler Transformation. By well-designed techniques in FRESCO, the memory usage can be controlled by users. A case study of micro-RNAs (miRNAs) was applied into FRESCO and the results showed that FRESCO can only used 268MB memory and mapped reads to all of known miRNAs and 98.6% novel miRNAs candidates.

Original languageEnglish
Title of host publicationProceedings - 2009 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2009
Pages232-237
Number of pages6
DOIs
StatePublished - 2009
Event2009 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2009 - Washington, DC, United States
Duration: 01 11 200904 11 2009

Publication series

NameProceedings - 2009 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2009

Conference

Conference2009 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2009
Country/TerritoryUnited States
CityWashington, DC
Period01/11/0904/11/09

Keywords

  • Approximate string matching
  • Burrows Wheeler Transformation
  • Hash look-up table algorithm
  • New sequencing techniques

Fingerprint

Dive into the research topics of 'Mapping short reads to a genome without using hash look-up table algorithm and Burrows Wheeler Transformation'. Together they form a unique fingerprint.

Cite this