Tuesday, 16th of February 2010 at 12:14:14 PM Introducing DOTUR, a Computer Program for Defining Operational Taxonomic Units and Estimating Species Richness
Patrick D. Schloss and Jo Handelsman, APPLIED AND ENVIRONMENTAL MICROBIOLOGY
Since we start to study metagenomics, to estimate species richness form complex samples become a major issue. Normally the 16S rRNA gene sequences identity is the target when we want to estimate the number of species within sample. Most of gene sequence in 16S rRNA is highly conserved between species but it also has several variance regions which can help us to distinguish different species. The goal of this paper is to help us to estimate the number of species within a sample. First step is multiple sequence alignment, they follow the sequence identity threshold which is normal used in the research but these criteria are still controversial. Sequences have >97% identity are same species, between 95% and 97% are same genus and between 80% and 95% are same phylum. DOTUR (Distance-Based OTU and Richness) assign each sequence into different operational taxonomic units (OTUs) based of sequence distance. DOTUR will calculate the Shannon-Weaver and Simpson diversity indices and estimate species richness within sample. They compare DOTUR result with other software, EstimateS, by using a clone library to validate their result. The results are similar to each other. There are several advantages in DOTUR, it runs faster and provide sequence alignment result which lack in EstimateS. DOTUR can produce different level of distance in separate files. They apply DOTUR to Amazonian soil sample which has 98 bacterial 16S rRNA in previous study. DOTUR reports there are 94 singleton and 2 doubletons which are total 96 OTUs. Then they apply DOTUR to the Sargasso Sea metagenome sequences. They reduce the sample set to two fragment sets; one is 690 partial 16S rRNA gene fragment and the other is 507 partial rpoB fragments as sample set. In 6% of sequence difference DOTUR report 114 16S rRNA and 304 rpoB. DOTUR has automatic, rapid and accurate features to estimate the richness of species within the sample. DOTUR can use different alignment algorithm and distances simultaneously to estimate the number of species more accurately.
Although DOTUR has some advantages, it can’t handle a large scale sample. Therefore it has been replace by MOTHUR. Unfortunately MOTHUR also have this issue. The performance
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