ReAlignerV: web-based genomic alignment tool with high specificity and robustness estimated by species-specific...

Area of Science:

• Genomics
• Bioinformatics
• Evolutionary Biology

Background:

• Conserved noncoding sequences (CNSs) across species identify functional genomic elements.
• Computational prediction of transcription factor binding sites (TFBSs) aids in identifying regulatory elements.
• Transposable elements (TEs) can influence gene regulatory network evolution, necessitating alignment methods robust to their insertions.

Purpose of the Study:

• To develop an alignment approach robust to TE insertions for discovering novel conserved TFBSs within TEs.
• To create a web server for complex alignment of genomic sequences incorporating TEs and TFBSs.

Main Methods:

• Construction of the ReAlignerV web server for genomic sequence alignment.
• Integration of predicted TFBSs and TE locations into alignment visualizations.
• Evaluation of alignment specificity and robustness using species-specific TEs (SSTEs) in sequences with high TE content.

Main Results:

• ReAlignerV provides schematic and pair-wise alignments displaying TFBSs and TEs.
• The tool demonstrates higher specificity and robustness to insertions compared to LAGAN, AVID, MAVID, and BLASTZ for sequences with >20% TE content.
• ReAlignerV successfully aligns TE-insertion-rich sequences without prior repeat masking.

Conclusions:

• ReAlignerV facilitates the identification of regulatory sequences within TEs, important for understanding regulatory network evolution.
• The tool increases the discovery potential of functional elements hidden in TEs.
• ReAlignerV is accessible online for public use and download.