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Open Access Highly Accessed Software

DNAAlignEditor: DNA alignment editor tool

Hector Sanchez-Villeda1*, Steven Schroeder14, Sherry Flint-Garcia2, Katherine E Guill2, Masanori Yamasaki13 and Michael D McMullen12

Author Affiliations

1 Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA

2 USDA-ARS, Plant Genetics Research Unit, Columbia, MO 65211, USA

3 Food Resources Education and Research Center, Kobe University, Hyogo, Japan

4 USDA-ARS Bovine Functional Genomics Laboratory, Beltsville, MD 20705, USA

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BMC Bioinformatics 2008, 9:154  doi:10.1186/1471-2105-9-154

Published: 19 March 2008



With advances in DNA re-sequencing methods and Next-Generation parallel sequencing approaches, there has been a large increase in genomic efforts to define and analyze the sequence variability present among individuals within a species. For very polymorphic species such as maize, this has lead to a need for intuitive, user-friendly software that aids the biologist, often with naïve programming capability, in tracking, editing, displaying, and exporting multiple individual sequence alignments. To fill this need we have developed a novel DNA alignment editor.


We have generated a nucleotide sequence alignment editor (DNAAlignEditor) that provides an intuitive, user-friendly interface for manual editing of multiple sequence alignments with functions for input, editing, and output of sequence alignments. The color-coding of nucleotide identity and the display of associated quality score aids in the manual alignment editing process. DNAAlignEditor works as a client/server tool having two main components: a relational database that collects the processed alignments and a user interface connected to database through universal data access connectivity drivers. DNAAlignEditor can be used either as a stand-alone application or as a network application with multiple users concurrently connected.


We anticipate that this software will be of general interest to biologists and population genetics in editing DNA sequence alignments and analyzing natural sequence variation regardless of species, and will be particularly useful for manual alignment editing of sequences in species with high levels of polymorphism.