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Conference Paper: IDBA-MTP: A Hybrid MetaTranscriptomic Assembler Based on Protein Information
Title | IDBA-MTP: A Hybrid MetaTranscriptomic Assembler Based on Protein Information |
---|---|
Authors | |
Keywords | assembling metatranscriptomic reads next-generation sequencing protein sequence alignment |
Issue Date | 2014 |
Publisher | Springer 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? |
Abstract | Metatranscriptomic 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/. |
Description | Lecture 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 Identifier | http://hdl.handle.net/10722/201112 |
ISBN | |
ISSN | 2023 SCImago Journal Rankings: 0.606 |
DC Field | Value | Language |
---|---|---|
dc.contributor.author | Leung, HCM | en_US |
dc.contributor.author | Yiu, SM | en_US |
dc.contributor.author | Chin, FYL | en_US |
dc.date.accessioned | 2014-08-21T07:13:35Z | - |
dc.date.available | 2014-08-21T07:13:35Z | - |
dc.date.issued | 2014 | en_US |
dc.identifier.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 | en_US |
dc.identifier.isbn | 9783319052687 | - |
dc.identifier.issn | 0302-9743 | - |
dc.identifier.uri | http://hdl.handle.net/10722/201112 | - |
dc.description | Lecture 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.abstract | Metatranscriptomic 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.language | eng | en_US |
dc.publisher | Springer Verlag. The Journal's web site is located at http://springerlink.com/content/105633/ | - |
dc.relation.ispartof | Lecture Notes in Computer Science | en_US |
dc.rights | The original publication is available at www.springerlink.com | - |
dc.subject | assembling | - |
dc.subject | metatranscriptomic reads | - |
dc.subject | next-generation sequencing | - |
dc.subject | protein sequence alignment | - |
dc.title | IDBA-MTP: A Hybrid MetaTranscriptomic Assembler Based on Protein Information | en_US |
dc.type | Conference_Paper | en_US |
dc.identifier.email | Leung, HCM: cmleung2@cs.hku.hk | en_US |
dc.identifier.email | Yiu, SM: smyiu@cs.hku.hk | en_US |
dc.identifier.email | Chin, FYL: chin@cs.hku.hk | en_US |
dc.identifier.authority | Leung, HCM=rp00144 | en_US |
dc.identifier.authority | Yiu, SM=rp00207 | en_US |
dc.identifier.authority | Chin, FYL=rp00105 | en_US |
dc.identifier.doi | 10.1007/978-3-319-05269-4_12 | - |
dc.identifier.scopus | eid_2-s2.0-84958521449 | - |
dc.identifier.hkuros | 235155 | en_US |
dc.identifier.volume | 8394 | - |
dc.identifier.spage | 160 | - |
dc.identifier.epage | 172 | - |
dc.publisher.place | Germany | - |
dc.identifier.issnl | 0302-9743 | - |