Multiple sequence alignment with user-dened constraints

Abstract: In many situations, automated multi-alignment programs are not able to correctly align families of nucleic acid or protein sequences. Distantly related se-quences are generally hard to align, and sequence duplications may present additional challenges to standard alignment algorithms. In the present paper, we describe a semi-automatic approach to multiple sequence alignment. The user can specify parts of the sequences that are thought to be related to each other; our software program will use these sites as anchor points and create a multiple alignment respecting these user-dened constraints. By using functionally, structurally or evolutionarily related po-sitions of the input sequences as anchor points, the proposed method can produce alignments that are biologically more meaningful than alignments produced by fully automated procedures. We apply our approach to genomic sequences around the Hox gene cluster. As a by-product, we obtain useful insights for the further development of alignment algorithms. The described alignment approach has been integrated into the tracker software system