NDLI: STITCH: Algorithm to Splice, Trim, Identify, Track, and Capture the Uniqueness of 16S rRNAs Sequence Pairs Using Public or In-house Database

Content Provider	Springer Nature Link
Author	Zhu, Dianhui Vaishampayan, Parag A. Venkateswaran, Kasthuri Fox, George E.
Copyright Year	2010
Abstract	A comparison of variable regions within the 16S rRNA gene is widely used to characterize relationships between bacteria and to identify phylogenetic affiliation of unknown bacteria. In environmental studies, polymerase chain reaction amplification of 16S rRNA followed by cloning and sequencing of numerous individual clones is an extensively used molecular method for elucidating microbial diversity. The sequencing process typically utilizes a forward and reverse primer pair to produce two partial reads (~700 to 800 base pairs each) that overlap and in total cover a large region of the full 16S rRNA sequence (~1.5 k base). In a typical application, this approach rapidly generates very large numbers of 16S rRNA datasets that can overwhelm manual processing efforts leading to both delays and errors. In particular, the approach presents two computational challenges: (1) the assembly of a composite sequence from the two partial reads and (2) the subsequent appropriate identification of the organism represented by the newly sequenced clones. Herein, we describe a software package, search, trim, identify, track, and capture the uniqueness of 16S rRNAs using public and in-house database (STITCH), which offers automated sequence pair splicing and genetic identification, thus simplifying the computationally intensive analysis of large sequencing libraries. The STITCH software is freely accessible over the Internet at: http://prion.bchs.uh.edu/stitch/.
Starting Page	669
Ending Page	675
Page Count	7
File Format	PDF
ISSN	00953628
Journal	Microbial Ecology
Volume Number	61
Issue Number	3
e-ISSN	1432184X
Language	English
Publisher	Springer-Verlag
Publisher Date	2010-11-27
Publisher Place	New York
Access Restriction	Subscribed
Subject Keyword	Microbial Ecology Ecology Microbiology Nature Conservation Geoecology/Natural Processes
Content Type	Text
Resource Type	Article
Subject	Soil Science Ecology Ecology, Evolution, Behavior and Systematics

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