SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

被引:1818
作者
Kopylova, Evguenia [1 ,2 ]
Noe, Laurent [1 ,2 ]
Touzet, Helene [1 ,2 ]
机构
[1] Univ Lille 1, UMR CNRS 8022, LIFL, F-59655 Villeneuve Dascq, France
[2] Inria Lille N Europe, F-59655 Villeneuve Dascq, France
关键词
SEQUENCE DATA; SEARCH; IDENTIFICATION; ALIGNMENT; ARB;
D O I
10.1093/bioinformatics/bts611
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
MOTIVATION: The application of next-generation sequencing (NGS) technologies to RNAs directly extracted from a community of organisms yields a mixture of fragments characterizing both coding and non-coding types of RNAs. The task to distinguish among these and to further categorize the families of messenger RNAs and ribosomal RNAs (rRNAs) is an important step for examining gene expression patterns of an interactive environment and the phylogenetic classification of the constituting species. RESULTS: We present SortMeRNA, a new software designed to rapidly filter rRNA fragments from metatranscriptomic data. It is capable of handling large sets of reads and sorting out all fragments matching to the rRNA database with high sensitivity and low running time.
引用
收藏
页码:3211 / 3217
页数:7
相关论文
共 25 条
[1]   BASIC LOCAL ALIGNMENT SEARCH TOOL [J].
ALTSCHUL, SF ;
GISH, W ;
MILLER, W ;
MYERS, EW ;
LIPMAN, DJ .
JOURNAL OF MOLECULAR BIOLOGY, 1990, 215 (03) :403-410
[2]  
[Anonymous], ACM J EXPT ALGORITHM, DOI [10.1145/1005813.1041517, DOI 10.1145/1005813.1041517]
[3]  
Askitis N., 2010, ACM JEA, V15, P7
[4]   Directed Culturing of Microorganisms Using Metatranscriptomics [J].
Bomar, Lindsey ;
Maltz, Michele ;
Colston, Sophie ;
Graf, Joerg .
MBIO, 2011, 2 (02)
[5]   The Comparative RNA Web (CRW) Site:: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs:: Correction (vol 3, pg 2, 2002) -: art. no. 15 [J].
Cannone, JJ ;
Subramanian, S ;
Schnare, MN ;
Collett, JR ;
D'Souza, LM ;
Du, YS ;
Feng, B ;
Lin, N ;
Madabusi, LV ;
Müller, KM ;
Pande, N ;
Shang, ZD ;
Yu, N ;
Gutell, RR .
BMC BIOINFORMATICS, 2002, 3 (1)
[6]   Profile hidden Markov models [J].
Eddy, SR .
BIOINFORMATICS, 1998, 14 (09) :755-763
[7]   Search and clustering orders of magnitude faster than BLAST [J].
Edgar, Robert C. .
BIOINFORMATICS, 2010, 26 (19) :2460-2461
[8]  
Gilbert JA, 2011, METHODS MOL BIOL, V733, P195, DOI 10.1007/978-1-61779-089-8_14
[9]   Burst tries: A fast, efficient data structure for string keys [J].
Heinz, S ;
Zobel, J ;
Williams, HE .
ACM TRANSACTIONS ON INFORMATION SYSTEMS, 2002, 20 (02) :192-223
[10]   Identification of ribosomal RNA genes in metagenomic fragments [J].
Huang, Ying ;
Gilna, Paul ;
Li, Weizhong .
BIOINFORMATICS, 2009, 25 (10) :1338-1340