BioMed Central Page 1 of 1 (page number not for citation purposes) BMC Bioinformatics Open Access Poster presentation Techniques for the analysis of trichome Pelagonium xhortorum expressed sequence tags Joseph Morris 1 , Eric Rouchka* 1 and David Schultz 2 Address: 1 Department of Computer Engineering and Computer Science, University of Louisville, Louisville, KY 40292, USA and 2 Department of Biology, University of Louisville, Louisville, KY 40292, USA Email: Eric Rouchka* - [email protected] * Corresponding author Background An important aspect of bioinformatics is the infrastructure for storage and display of high throughput sequence data generated by biologists. The construction of databases and applications to display the results in a meaningful and useful way is not a trivial task. A well-designed and exe- cuted system can vastly improve the results obtained from an experiment. We present a system for storing and view- ing EST sequences based on a set generated for a geranium genome. Results A series of over 4,000 expressed-sequence tags (ESTs) orig- inating from the trichome of the geranium, Pelagonium xhortorum, were generated in a wet lab. EST sequences were organized into clusters of overlapping sequences using CAP3. The resulting clusters, including single EST clusters, were analyzed and annotated by hand in order to classify the sequences into families and subfamilies of genes. Further refinement using Blast2GO classifies these sequences into annotated groups based on biological process, cellular component, and molecular function. Presentation of the results were accomplished through a MySQL database and java servlet web pages used to ana- lyze, group, and display the resulting data. Queries into the data can be performed by using blast or by searching by known gene families. Acknowledgements This work was supported in part by NIH-NCRR Grant P20RR16481 and NIH-NIEHS Grant P30ES014443. Its contents are solely the responsibility of the authors and do not represent the official views of NCRR, NIEHS, or NIH. from UT-ORNL-KBRIN Bioinformatics Summit 2008 Cadiz, KY, USA. 28–30 March 2008 Published: 8 July 2008 BMC Bioinformatics 2008, 9(Suppl 7):P25 doi:10.1186/1471-2105-9-S7-P25 <supplement> <title> <p>UT-ORNL-KBRIN Bioinformatics Summit 2008</p> </title> <editor>Eric C Rouchka and Julia Krushkal</editor> <note>Meeting abstracts – A single PDF containing all abstracts in this Supplement is available <a href="http://www.biomedcentral.com/content/pdf/1471-2105-9-S7-full.pdf">here</a>.</note> <url>http://www.kbrin.louisville.edu/summit/</url> </supplement> This abstract is available from: http://www.biomedcentral.com/1471-2105/9/S7/P25 © 2008 Morris et al; licensee BioMed Central Ltd.

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Page 1: Techniques for the analysis of trichome Pelagonium xhortorum expressed sequence tags

BioMed Central

Page 1 of 1(page number not for citation purposes)

BMC Bioinformatics

Open AccessPoster presentationTechniques for the analysis of trichome Pelagonium xhortorum expressed sequence tagsJoseph Morris1, Eric Rouchka*1 and David Schultz2

Address: 1Department of Computer Engineering and Computer Science, University of Louisville, Louisville, KY 40292, USA and 2Department of Biology, University of Louisville, Louisville, KY 40292, USA

Email: Eric Rouchka* - [email protected]

* Corresponding author

BackgroundAn important aspect of bioinformatics is the infrastructurefor storage and display of high throughput sequence datagenerated by biologists. The construction of databases andapplications to display the results in a meaningful anduseful way is not a trivial task. A well-designed and exe-cuted system can vastly improve the results obtained froman experiment. We present a system for storing and view-ing EST sequences based on a set generated for a geraniumgenome.

ResultsA series of over 4,000 expressed-sequence tags (ESTs) orig-inating from the trichome of the geranium, Pelagoniumxhortorum, were generated in a wet lab. EST sequenceswere organized into clusters of overlapping sequencesusing CAP3. The resulting clusters, including single ESTclusters, were analyzed and annotated by hand in order toclassify the sequences into families and subfamilies ofgenes. Further refinement using Blast2GO classifies thesesequences into annotated groups based on biologicalprocess, cellular component, and molecular function.Presentation of the results were accomplished through aMySQL database and java servlet web pages used to ana-lyze, group, and display the resulting data. Queries intothe data can be performed by using blast or by searchingby known gene families.

AcknowledgementsThis work was supported in part by NIH-NCRR Grant P20RR16481 and NIH-NIEHS Grant P30ES014443. Its contents are solely the responsibility of the authors and do not represent the official views of NCRR, NIEHS, or NIH.

from UT-ORNL-KBRIN Bioinformatics Summit 2008Cadiz, KY, USA. 28–30 March 2008

Published: 8 July 2008

BMC Bioinformatics 2008, 9(Suppl 7):P25 doi:10.1186/1471-2105-9-S7-P25

<supplement> <title> <p>UT-ORNL-KBRIN Bioinformatics Summit 2008</p> </title> <editor>Eric C Rouchka and Julia Krushkal</editor> <note>Meeting abstracts – A single PDF containing all abstracts in this Supplement is available <a href="http://www.biomedcentral.com/content/pdf/1471-2105-9-S7-full.pdf">here</a>.</note> <url>http://www.kbrin.louisville.edu/summit/</url> </supplement>

This abstract is available from: http://www.biomedcentral.com/1471-2105/9/S7/P25

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