Figure 1

An overview of the ReAlignerV web service. Through the input webpage (A), users can input the query sequences, their annotation data and parameters. The ReAlignerV server returns the schematic alignments for 2-species (B) or 3-species (C) comparisons with or without graphs of the GC and ATGC contents. In the results, the aligned blocks are shown by blue-color-coded boxes. The results pages still hold the windows for annotations so that users can modify the results presentation interactively through this web service after the alignment procedure. Once the alignment computation has been done, the annotation processes are quick. An enlarged snapshot (D) of the schematic alignment shows how the predicted TFBS and TEs are integrated and the locations of predicted TFBS are indicated by red and blue ticks with their names in the same colors. Green horizontal bars along the alignment lines designate the positions of TEs (D). From both the 2- and 3-species ReAlignerV results pages, users can jump to a pair-wise alignment (E), where the predicted TFBS sequences are also shown alongside each aligned sequence.