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Conference Paper: IDBA-MTP: A Hybrid MetaTranscriptomic Assembler Based on Protein Information

TitleIDBA-MTP: A Hybrid MetaTranscriptomic Assembler Based on Protein Information
Authors
Issue Date2014
PublisherSpringer Verlag. The Journal's web site is located at http://springerlink.com/content/105633/
Citation
The 18th Annual International Conference, (RECOMB 2014), Pittsburgh, USA, 2-5 April 2014. In Lecture Notes in Computer Science, 2014, v. 8394, p. 160-172 How to Cite?
AbstractMetatranscriptomic analysis provides information on how a microbial community reacts to environmental changes. Using next-generation sequencing (NGS) technology, biologists can study microbe community by sampling short reads from a mixture of mRNAs (metatranscriptomic data). As most microbial genome sequences are unknown, it would seem that de novo assembly of the mRNAs is needed. However, NGS reads are short and mRNAs share many similar regions and differ tremendously in abundance levels, making de novo assembly challenging. The existing assembler, IDBA-MT, designed specifically for the assembly of metatranscriptomic data only performs well on high-expressed mRNAs. This paper introduces IDBA-MTP, which adopts a novel approach to metatranscriptomic assembly that makes use of the fact that there is a database of millions of known protein sequences associated with mRNAs. How to effectively use the protein information is non-trivial given the size of the database and given that different mRNAs might lead to proteins with similar functions (because different amino acids might have similar characteristics). IDBA-MTP employs a similarity measure between mRNAs and protein sequences, dynamic programming techniques and seed-and-extend heuristics to tackle the problem effectively and efficiently. Experimental results show that IDBA-MTP outperforms existing assemblers by reconstructing 14% more mRNAs. Availability: www.cs.hku.hk/alse/hkubrg/.
DescriptionLecture Notes in Computer Science, vol 8394 entitled: Research in Computational Molecular Biology: 18th Annual International Conference, RECOMB 2014, Pittsburgh, PA, USA, April 2-5, 2014: Proceedings
Persistent Identifierhttp://hdl.handle.net/10722/201112
ISBN
ISSN
2005 Impact Factor: 0.402
2015 SCImago Journal Rankings: 0.252

 

DC FieldValueLanguage
dc.contributor.authorLeung, HCMen_US
dc.contributor.authorYiu, SMen_US
dc.contributor.authorChin, FYLen_US
dc.date.accessioned2014-08-21T07:13:35Z-
dc.date.available2014-08-21T07:13:35Z-
dc.date.issued2014en_US
dc.identifier.citationThe 18th Annual International Conference, (RECOMB 2014), Pittsburgh, USA, 2-5 April 2014. In Lecture Notes in Computer Science, 2014, v. 8394, p. 160-172en_US
dc.identifier.isbn9783319052687-
dc.identifier.issn0302-9743-
dc.identifier.urihttp://hdl.handle.net/10722/201112-
dc.descriptionLecture Notes in Computer Science, vol 8394 entitled: Research in Computational Molecular Biology: 18th Annual International Conference, RECOMB 2014, Pittsburgh, PA, USA, April 2-5, 2014: Proceedings-
dc.description.abstractMetatranscriptomic analysis provides information on how a microbial community reacts to environmental changes. Using next-generation sequencing (NGS) technology, biologists can study microbe community by sampling short reads from a mixture of mRNAs (metatranscriptomic data). As most microbial genome sequences are unknown, it would seem that de novo assembly of the mRNAs is needed. However, NGS reads are short and mRNAs share many similar regions and differ tremendously in abundance levels, making de novo assembly challenging. The existing assembler, IDBA-MT, designed specifically for the assembly of metatranscriptomic data only performs well on high-expressed mRNAs. This paper introduces IDBA-MTP, which adopts a novel approach to metatranscriptomic assembly that makes use of the fact that there is a database of millions of known protein sequences associated with mRNAs. How to effectively use the protein information is non-trivial given the size of the database and given that different mRNAs might lead to proteins with similar functions (because different amino acids might have similar characteristics). IDBA-MTP employs a similarity measure between mRNAs and protein sequences, dynamic programming techniques and seed-and-extend heuristics to tackle the problem effectively and efficiently. Experimental results show that IDBA-MTP outperforms existing assemblers by reconstructing 14% more mRNAs. Availability: www.cs.hku.hk/alse/hkubrg/.-
dc.languageengen_US
dc.publisherSpringer Verlag. The Journal's web site is located at http://springerlink.com/content/105633/-
dc.relation.ispartofLecture Notes in Computer Scienceen_US
dc.rightsThe original publication is available at www.springerlink.com-
dc.titleIDBA-MTP: A Hybrid MetaTranscriptomic Assembler Based on Protein Informationen_US
dc.typeConference_Paperen_US
dc.identifier.emailLeung, HCM: cmleung2@cs.hku.hken_US
dc.identifier.emailYiu, SM: smyiu@cs.hku.hken_US
dc.identifier.emailChin, FYL: chin@cs.hku.hken_US
dc.identifier.authorityLeung, HCM=rp00144en_US
dc.identifier.authorityYiu, SM=rp00207en_US
dc.identifier.authorityChin, FYL=rp00105en_US
dc.identifier.doi10.1007/978-3-319-05269-4_12-
dc.identifier.scopuseid_2-s2.0-84898952181-
dc.identifier.hkuros235155en_US
dc.identifier.volume8394-
dc.identifier.spage160-
dc.identifier.epage172-
dc.publisher.placeGermany-

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