title: DNAAlignEditor: DNA alignment editor tool.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors: Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA. sanchezvilledah@missouri.edu
authors: Hector
authors: H
authors: Sanchez-Villeda
authors: Steven
authors: S
authors: Schroeder
authors: Sherry
authors: S
authors: Flint-Garcia
authors: Katherine E
authors: KE
authors: Guill
authors: Masanori
authors: M
authors: Yamasaki
authors: Michael D
authors: MD
authors: McMullen
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014584:User-Computer Interface; D015443:Word Processing / Q000379:methods