title: Indelign: a probabilistic framework for annotation of insertions and deletions in a multiple alignment.
abstract: BACKGROUND
  A quantitative study of molecular evolutionary events such as substitutions, insertions and deletions from closely related genomes requires (1) an accurate multiple sequence alignment program and (2) a method to annotate the insertions and deletions that explain the 'gaps' in the alignment. Although the former requirement has been extensively addressed, the latter problem has received little attention, especially in a comprehensive probabilistic framework.
  
  
  RESULTS
  Here, we present Indelign, a program that uses a probabilistic evolutionary model to compute the most likely scenario of insertions and deletions consistent with an input multiple alignment. It is also capable of modifying the given alignment so as to obtain a better agreement with the evolutionary model. We find close to optimal performance and substantial improvement over alternative methods, in tests of Indelign on synthetic data. We use Indelign to analyze regulatory sequences in Drosophila, and find an excess of insertions over deletions, which is different from what has been reported for neutral sequences.
  
  
  BACKGROUND
  The Indelign program may be downloaded from the website http://veda.cs.uiuc.edu/indelign/
  
  
  BACKGROUND
  Supplementary material is available at Bioinformatics online.
authors.affiliation: Department of Computer Science, University of Illinois, Urbana-Champaign, Urbana, IL, USA.
authors.forename: Jaebum
authors.initials: J
authors.lastname: Kim
authors.forename: Saurabh
authors.initials: S
authors.lastname: Sinha
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D003198:Computer Simulation; D004252:DNA Mutational Analysis / Q000379:methods*; D004251:DNA Transposable Elements / Q000235:genetics*; D003627:Data Interpretation, Statistical; D019143:Evolution, Molecular; D008957:Models, Genetic; D015233:Models, Statistical; D008969:Molecular Sequence Data; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D017384:Sequence Deletion / Q000235:genetics*; D012984:Software
chemical_list: D004251:DNA Transposable Elements