title: ReAlignerV: web-based genomic alignment tool with high specificity and robustness estimated by species-specific insertion sequences.
abstract: BACKGROUND
  Detecting conserved noncoding sequences (CNSs) across species highlights the functional elements. Alignment procedures combined with computational prediction of transcription factor binding sites (TFBSs) can narrow down key regulatory elements. Repeat masking processes are often performed before alignment to mask insertion sequences such as transposable elements (TEs). However, recently such TEs have been reported to influence the gene regulatory network evolution. Therefore, an alignment approach that is robust to TE insertions is meaningful for finding novel conserved TFBSs in TEs.
  
  
  RESULTS
  We constructed a web server 'ReAlignerV' for complex alignment of genomic sequences. ReAlignerV returns ladder-like schematic alignments that integrate predicted TFBSs and the location of TEs. It also provides pair-wise alignments in which the predicted TFBS sites and their names are shown alongside each sequence. Furthermore, we evaluated false positive aligned sites by focusing on the species-specific TEs (SSTEs), and found that ReAlignerV has a higher specificity and robustness to insertions for sequences having more than 20% TE content, compared to LAGAN, AVID, MAVID and BLASTZ.
  
  
  CONCLUSIONS
  ReAlignerV can be applied successfully to TE-insertion-rich sequences without prior repeat masking, and this increases the chances of finding regulatory sequences hidden in TEs, which are important sources of the regulatory network evolution. ReAlignerV can be accessed through and downloaded from http://genet.med.kagawa-u.ac.jp/.
authors.affiliation: Life Science Research Center, Kagawa University, Ikenobe 1750-1, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan. iwama@med.kagawa-u.ac.jp
authors.forename: Hisakazu
authors.initials: H
authors.lastname: Iwama
authors.forename: Yukio
authors.initials: Y
authors.lastname: Hori
authors.forename: Kensuke
authors.initials: K
authors.lastname: Matsumoto
authors.forename: Koji
authors.initials: K
authors.lastname: Murao
authors.forename: Toshihiko
authors.initials: T
authors.lastname: Ishida
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D004251:DNA Transposable Elements / Q000235:genetics*; D020407:Internet; D008969:Molecular Sequence Data; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D013045:Species Specificity
chemical_list: D004251:DNA Transposable Elements