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

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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/.

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Acknowledgment

The research described in this publication was carried out in part at the Jet Propulsion Laboratory, California Institute of Technology, under a contract with the National Aeronautics and Space Administration and in part at the University of Houston under a subcontract from the Jet Propulsion Laboratory.

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Author notes

  1. Dianhui Zhu

    Present address: Human Genome Sequencing Center, Baylor College of Medicine, Room Alkek N1619, Houston, TX, 77030, USA

Authors and Affiliations

  1. Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA

    Dianhui Zhu & George E. Fox

  2. Biotechnology and Planetary Protection Group, California Institute of Technology, Jet Propulsion Laboratory, M/S 89-102, 4800 Oak Grove Dr, Pasadena, CA, 91109, USA

    Parag A. Vaishampayan & Kasthuri Venkateswaran

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  1. Dianhui Zhu
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  2. Parag A. Vaishampayan
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Correspondence to Parag A. Vaishampayan.

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Zhu, D., Vaishampayan, P.A., Venkateswaran, K. et al. STITCH: Algorithm to Splice, Trim, Identify, Track, and Capture the Uniqueness of 16S rRNAs Sequence Pairs Using Public or In-house Database. Microb Ecol 61, 669–675 (2011). https://doi.org/10.1007/s00248-010-9779-2

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