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Techniques for the analysis of trichome Pelagonium xhortorum expressed sequence tags


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 executed system can vastly improve the results obtained from an experiment. We present a system for storing and viewing EST sequences based on a set generated for a geranium genome.


A series of over 4,000 expressed-sequence tags (ESTs) originating 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 analyze, group, and display the resulting data. Queries into the data can be performed by using blast or by searching by known gene families.


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.

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Correspondence to Eric Rouchka.

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Open Access This article is published under license to BioMed Central Ltd. This is an Open Access article is distributed under the terms of the Creative Commons Attribution License ( ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Morris, J., Rouchka, E. & Schultz, D. Techniques for the analysis of trichome Pelagonium xhortorum expressed sequence tags. BMC Bioinformatics 9 (Suppl 7), P25 (2008).

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