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ARS Home » Midwest Area » Columbia, Missouri » Plant Genetics Research » Research » Publications at this Location » Publication #201199

Title: DNA Align Editor: DNA Alignment Editor Tool

item Flint-Garcia, Sherry
item Guill, Katherine
item McMullen, Michael

Submitted to: Bioinformatics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/19/2008
Publication Date: 3/19/2008
Citation: Sanchez-Villeda, H., Schroeder, S., Flint Garcia, S.A., Guill, K.E., Yamasaki, M., McMullen, M.D. 2008. DNA align editor: DNA alignment editor tool. Bioinformatics. 9:154.

Interpretive Summary: Currently available DNA sequence alignment tools are difficult or ineffective to use on highly polymorphic species such as corn. To aid in refining DNA sequence alignments to correctly identify sequence polymorphism, a new, intuitive, user-friendly sequence alignment editing tool was developed. An intrinsic feature of the tool is display of sequence quality to aid editing decisions. This tool will be useful to molecular and population genetics for corn and other highly polymorphic species enhancing speed and accuracy of identification of sequence polymorphism for genetic marker development and trait analysis.

Technical Abstract: The SNPAlignEditor is a DNA sequence alignment editor that runs on Windows platforms. The purpose of the program is to provide an intuitive, user-friendly tool for manual editing of multiple sequence alignments by providing functions for input, editing, and output of nucleotide sequence alignments. It works as a client/server tool having two main components: a relational database (DBSNP) as back-end which collects all the processed alignments and a windows-based user interface as front-end connected with the back-end through object data base connectivity (ODBC) drivers. SNPAlignEditor can be used either as stand-alone application or as network application with multiple users concurrently connected.