Progressive multiple alignment with constraints

A progressive alignment algorithm produces a multi-alignment of a set of sequences by repeatedly aligning pairs of sequences and/or previously generated alignments. We describe a method for guaranteeing that the alignment generated by a progressivealignment strategy satisfies a user-specified collection of constraints about where certain sequence positions should appear relative to others. Given a collection of ¢ constraints over £ sequences whose total length is ¤ , our algorithm takes ¥ ¦ £ ¦ ¤ § ¨ £ ¢ © © time. An alignment of the  -like globin gene clusters of several mammals illustrates the practicality of the method. Key words: Multiplesequence alignment, constrainedalignment, dynamic programming

• Type: Conference
• Year: 1997
• Where: RECOMB
• Authors: Gene Myers, Sanford Selznick, Zheng Zhang 0004, Webb Miller
• Keywords: Certain Sequence Positions, Computational Biology, Progressive Alignment Algorithm, RECOMB 1997, Sequences