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This article is part of the supplement: UT-ORNL-KBRIN Bioinformatics Summit 2010

Open Access Poster presentation

Sequence and annotation of the Wizard007 mycobacterium phage genome

Ejike Anyanwu, Kaitlyn Cole, Karlee Driver, Anthony Falcone, Elizabeth Farnsworth, Benjamin Howard, Brittney Howard, Courtney Howard, Rodney King, Jordan Olberding, Mackenzie Perkins, Claire Rinehart*, Heidi Sayre, Tyler Scaff, Sarah Schrader, Prasanna Tamarapu Parthasarathy and Cynthia Tope

Author Affiliations

Department of Biology, Western Kentucky University, Bowling Green, KY 42101, USA

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BMC Bioinformatics 2010, 11(Suppl 4):P15  doi:10.1186/1471-2105-11-S4-P15


The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1471-2105/11/S4/P15


Published:23 July 2010

© 2010 Rinehart et al; licensee BioMed Central Ltd.

Material and methods

The Wizard007 bacteriophage was isolated from a soil sample taken at N36° 49’36.8” W87° 29’42.5” in Hopkinsville, KY. It was plaque purified on Mycobacterium smegmatis and DNA was isolated using the Promega Wizard DNA purification kit. The DNA was sequenced at the Virginia Commonwealth University by Roche 454 DNA sequencing. The genome quality was confirmed in Consed [1] and found to be 51,034 bp in length. Genes were called from the assembled sequence with a workflow consisting of Glimmer [2], GeneMark [3], tRNAscan [4], and SDFinder to identify potential gene features. Gbrowse [5], Apollo [6], and BLAST [7] were used to call and annotate genes. A 10 base 3’ overhang was found at the ends by ligating the genomic DNA and sequencing a PCR product produced across the ligated ends.

Results and conclusion

Wizard007 is 95% similar to the Mycobacterium phage Peaches (NC_013694) when comparing the number of gene BLAST hits. The first 41,000 bp and the genes contained therein match Peaches’ organization and sequence very closely. The 3’ end of Wizard007 lacks 4 coding sequences that are found in Peaches (CDS 69, 74, 75, & 78) and it has one coding sequence that is not called in Peaches (gp 76). Additionally there are two coding sequences in Peaches (CDS 83 & 84) that do not match Wizard007 (gp 77 & 79).

Acknowledgements

Funding for the DNA sequencing of Wizard007 was provided by the WKU Bioinformatics and Information Science Center. Supplies and technical support for the isolation and genome annotation were provided by the Howard Hughes Medical Institute Science Education Alliance National Genome Research Initiative.

References

  1. Gordon D, Abajian C, Green P: Consed: A Graphical Tool for Sequence Finishing.

    Genome Research 1998, 8:195-202. PubMed Abstract | Publisher Full Text OpenURL

  2. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL: Improved microbial gene identification with GLIMMER.

    Nucleic Acids Research 1999, 27:4636-4641. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  3. Besemer J, Lomsadze A, Borodovsky M: GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions.

    Nucleic Acids Research 2001, 29:2607-2618. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  4. Lowe TM, Eddy SR: tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.

    Nucleic Acids Research 1997, 25:955-964. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  5. Stein LD, Mungall C, Shu S, Caudy M, Mangone M, Day A, Nickerson E, Stajich JE, Harris TW, Arva A, Lewis S: The generic genome browser: a building block for a model organism system database.

    Genome Res. 2002, 12:1599-610. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  6. Lewis SE, Searle SMJ, Harris N, Gibson M, Iyer V, Ricter J, Wiel C, Bayraktaroglu L, Birney E, Crosby MA, Kaminker JS, Matthews B, Prochnik SE, Smith CD, Tupy JL, Rubin GM, Misra S, Mungall CJ, Clamp ME: Apollo: a sequence annotation editor.

    Genome Biol 2002, 3:RESEARCH0082.

    research

    PubMed Abstract | BioMed Central Full Text | PubMed Central Full Text OpenURL

  7. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool.

    J. Mol. Biol 1990, 215:403-410. PubMed Abstract OpenURL