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Global Assembly of Expressed Sequence Tags

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RNA Abundance Analysis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 883))

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Abstract

The method for the construction of Expressed Sequence Tag (EST) assemblies described here uses reads generated from 454 pyrosequencing and Sanger and Illumina (Solexa) sequencing technologies as input. It is consistent with and parallels many established EST assembly protocols, for example the TIGR Gene Indices. Reads that are used as input to the EST assembly process usually come from both internal and external sources. Thus, in addition to internally generated EST reads, expressed transcripts are collected from dbEST and also the NCBI GenBank nucleotide database (full-length and partial cDNAs). “Virtual” transcript sequences derived from whole genome annotation projects can be excluded, depending on the needs of the project. Currently, in most cases, 454-derived sequences can be treated similar to Sanger-derived ESTs. In contrast, the shorter Solexa-derived sequences will have to undergo a round of either de novo assembly or an “align-then-assemble” approach against a reference genome, if available, before these transcripts can be used for the purpose of a global EST assembly that combines a mixture of Sanger and next-generation sequencing technologies.

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Acknowledgments

The author wishes to acknowledge funding and support from the NIH/NHLBI Center for Human Immunology.

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Authors and Affiliations

  1. Center for Human Immunology, Autoimmunity, and Inflammation, National Institute of Health, Bethesda, MD, USA

    Foo Cheung

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  1. Foo Cheung
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Correspondence to Foo Cheung .

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Editors and Affiliations

  1. , Dept. Plant Pathology & Microbiology, University of California, University Avenue 900, Riverside, 92521, USA

    Hailing Jin

  2. , Division of Plant Sciences, University of Missouri, Agriculture Building 1-31, Columbia, 65211, Missouri, USA

    Walter Gassmann

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Cheung, F. (2012). Global Assembly of Expressed Sequence Tags. In: Jin, H., Gassmann, W. (eds) RNA Abundance Analysis. Methods in Molecular Biology, vol 883. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-839-9_15

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  • DOI: https://doi.org/10.1007/978-1-61779-839-9_15

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-61779-838-2

  • Online ISBN: 978-1-61779-839-9

  • eBook Packages: Springer Protocols

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