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

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 foc...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Hisakazu Iwama, Yukio Hori, Kensuke Matsumoto, Koji Murao, Toshihiko Ishida
• Keywords: BMCBI 2008, Functional Elements, Regulatory Network Evolution, Sequences