APPLYING CONCEPTUAL MODELING TO ALIGNMENT TOOLS ONE STEP TOWARDS THE AUTOMATION OF DNA SEQUENCE ANALYSIS

Maria José Villanueva, Francisco Valverde, Oscar Pastor

2011

Abstract

Nowadays, the search of variations in DNA samples according to a reference sequence is performed using several bioinformatic tools. Due to the process complexity, none of these tools fulfill all the functionality required by biologists. For that reason, the definition of an integration process between these different tools becomes a mandatory requirement. One interesting issue is that bioinformatic tools do not comply with any standard format for expressing the output reports. As a consequence, the flow among tools must be manually solved. This paper proposes a conceptual model in order to formalize how the output from alignment tools must be produced. This work also provides a textual format based on this conceptual model. Thanks to both contributions, the integration is handled in the problem space and the related technological details are avoided. As a proof of concept of these ideas, the proposed format has been applied in a DNA sequence analysis process which uses two bioinformatic tools.

Paper Citation

in Harvard Style

Villanueva M., Valverde F. and Pastor O. (2011). APPLYING CONCEPTUAL MODELING TO ALIGNMENT TOOLS ONE STEP TOWARDS THE AUTOMATION OF DNA SEQUENCE ANALYSIS . In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2011) ISBN 978-989-8425-36-2, pages 137-142. DOI: 10.5220/0003142001370142

in Bibtex Style

@conference{bioinformatics11,
author={Maria José Villanueva and Francisco Valverde and Oscar Pastor},
title={APPLYING CONCEPTUAL MODELING TO ALIGNMENT TOOLS ONE STEP TOWARDS THE AUTOMATION OF DNA SEQUENCE ANALYSIS},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2011)},
year={2011},
pages={137-142},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003142001370142},
isbn={978-989-8425-36-2},
}

in EndNote Style

TY - CONF
JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2011)
TI - APPLYING CONCEPTUAL MODELING TO ALIGNMENT TOOLS ONE STEP TOWARDS THE AUTOMATION OF DNA SEQUENCE ANALYSIS
SN - 978-989-8425-36-2
AU - Villanueva M.
AU - Valverde F.
AU - Pastor O.
PY - 2011
SP - 137
EP - 142
DO - 10.5220/0003142001370142