title: IDBA-MTP: A Hybrid Metatranscriptomic Assembler Based on Protein Information.
abstract: Metatranscriptomic analysis provides information on how a microbial community reacts to environmental changes. Using next-generation sequencing (NGS) technology, biologists can study the 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 and performs well only on high-expressed mRNAs. This article 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 nontrivial 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.
authors.affiliation: Department of Computer Science, The University of Hong Kong , Hong Kong , Hong Kong.
authors.forename: Henry C M
authors.initials: HC
authors.lastname: Leung
authors.forename: Siu-Ming
authors.initials: SM
authors.lastname: Yiu
authors.forename: Francis Y L
authors.initials: FY
authors.lastname: Chin
mesh_terms: D000465:Algorithms; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics; D020451:Contig Mapping / Q000379:methods / Q000706:statistics & numerical data*; D057225:Data Mining; D059014:High-Throughput Nucleotide Sequencing; D056186:Metagenomics / Q000379:methods / Q000706:statistics & numerical data; D059013:Microbial Consortia / Q000235:genetics*; D020543:Proteome / Q000737:chemistry / Q000235:genetics; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics; D012333:RNA, Messenger / Q000737:chemistry* / Q000235:genetics; D017422:Sequence Analysis, DNA; D012984:Software; D059467:Transcriptome
chemical_list: D001426:Bacterial Proteins; D020543:Proteome; D012329:RNA, Bacterial; D012333:RNA, Messenger
keywords: assembling; metatranscriptomic reads; next-generation sequencing; protein sequence alignment