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Generating Unigene Collections of Expressed Sequence Tag Sequences for Use in Mass Spectrometry Identification

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Mass Spectrometry Data Analysis in Proteomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 367))

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Abstract

Expressed sequence tag sequences remain the largest resource of DNA sequence for most organisms despite recent advances in genome sequencing. These sequences are short, fragmented versions of the expressed genes. By DNA sequence assembly, the fragments can be assembled into contiguous DNA sequences that are better suited for protein identification by mass spectrometry.

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References

  1. Boguski, M. S., Lowe, T. M., and Tolstoshev, C. M. (1993) dbEST—database for “expressed sequence tags”. Nat. Genet. 4, 332–333.

    Article  PubMed  CAS  Google Scholar 

  2. Mann, M., Hendrickson, R. C., and Pandey, A. (2001) Analysis of proteins and proteomes by mass spectrometry. Annu. Rev. Biochem. 70, 437–473.

    Article  PubMed  CAS  Google Scholar 

  3. Slater, G. C. (1999) Expressed sequence tag analysis tools. PhD thesis, March 3, 2006. Human Genome Mapping Project RC, Hinxton, Cambridge, UK.

    Google Scholar 

  4. Liang, F., Holt, I., Pertea, G., Karamycheva, S., Salzberg, S. L., and Quackenbush, J. (2000) An optimized protocol for analysis of EST sequences. Nucl. Acids Res. 18, 3657–3665.

    Article  Google Scholar 

  5. Pertea, G., Huang, X., Liang, F., et al. (2003) TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 19, 651–652.

    Article  PubMed  CAS  Google Scholar 

  6. Wheeler, D. L., Church, D. M., Federhen, S. L., et al. (2003) Database resources of the national center for biotechnology. Nucleic Acids Res. 31, 28–33.

    Article  PubMed  CAS  Google Scholar 

  7. Ewing, B. and Green, P. (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8, 186–194.

    PubMed  CAS  Google Scholar 

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© 2007 Humana Press Inc., Totowa, NJ

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Emmersen, J. (2007). Generating Unigene Collections of Expressed Sequence Tag Sequences for Use in Mass Spectrometry Identification. In: Matthiesen, R. (eds) Mass Spectrometry Data Analysis in Proteomics. Methods in Molecular Biology, vol 367. Humana Press. https://doi.org/10.1385/1-59745-275-0:77

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  • DOI: https://doi.org/10.1385/1-59745-275-0:77

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-563-7

  • Online ISBN: 978-1-59745-275-5

  • eBook Packages: Springer Protocols

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