ReAlignerV: Web-based genomic alignment tool with high specificity and robustness estimated by species-specific insertion sequences

Hisakazu Iwama¹^,2 , Yukio Hori³ , Kensuke Matsumoto⁴ , Koji Murao⁴ and Toshihiko Ishida⁴

¹Life Science Research Center, Kagawa University, Ikenobe 1750-1, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan

²Faculty of Medicine, Kagawa University, Ikenobe 1750-1, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan

³Information Technology Center, Saiwai-cho Branch Office, Kagawa University, 2-1 Saiwai-cho, Takamatsu-shi, Kagawa, 760-8521 Japan

⁴Division of Endocrinology and Metabolism, Department of Internal Medicine, Faculty of Medicine, Kagawa University, Ikenobe 1750-1, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan

author email corresponding author email

BMC Bioinformatics 2008, 9:112doi:10.1186/1471-2105-9-112


Published:	22 February 2008

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.

Conclusion

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/ webcite.