Max-Planck-Institut für Informatik
max planck institut
informatik
mpii logo Minerva of the Max Planck Society
 

MPI-I-96-1-028

A branch-and-cut algorithm for multiple sequence alignment

Reinert, Knut and Lenhof, Hans-Peter and Mutzel, Petra and Mehlhorn, Kurt and Kececioglou, John D.

MPI-I-96-1-028. November 1996, 15 pages. | Status: available - back from printing | Next --> Entry | Previous <-- Entry

Abstract in LaTeX format:
Multiple sequence alignment is an important problem in computational biology.
We study the Maximum Trace formulation introduced by
Kececioglu~\cite{Kececioglu91}.
We first phrase the problem in terms of forbidden subgraphs,
which enables us to express Maximum Trace as an integer linear-programming
problem,
and then solve the integer linear program using methods from polyhedral
combinatorics.
The trace {\it polytope\/} is the convex hull of all feasible solutions
to the Maximum Trace problem;
for the case of two sequences,
we give a complete characterization of this polytope.
This yields a polynomial-time algorithm
for a general version of pairwise sequence alignment
that, perhaps suprisingly, does not use dynamic programming;
this yields, for instance, a non-dynamic-programming algorithm for
sequence comparison under the 0-1 metric,
which gives another answer to a long-open question in the area of string algorithms
\cite{PW93}.
For the multiple-sequence case,
we derive several classes of facet-defining inequalities
and show that for all but one class, the corresponding separation problem
can be solved in polynomial time.
This leads to a branch-and-cut algorithm for multiple sequence alignment,
and we report on our first computational experience.
It appears that a polyhedral approach to multiple sequence alignment
can solve instances that are beyond present dynamic-programming approaches.

Acknowledgement:
References to related material:

To download this research report, please select the type of document that fits best your needs.Attachement Size(s):
MPI-I-96-1-028.ps202 KBytes
Please note: If you don't have a viewer for PostScript on your platform, try to install GhostScript and GhostView
URL to this document: http://domino.mpi-inf.mpg.de/internet/reports.nsf/NumberView/1996-1-028
Hide details for BibTeXBibTeX
@TECHREPORT{ReinertLenhofMutzelMehlhornKececioglou96,
  AUTHOR = {Reinert, Knut and Lenhof, Hans-Peter and Mutzel, Petra and Mehlhorn, Kurt and Kececioglou, John D.},
  TITLE = {A branch-and-cut algorithm for multiple sequence alignment},
  TYPE = {Research Report},
  INSTITUTION = {Max-Planck-Institut f{\"u}r Informatik},
  ADDRESS = {Im Stadtwald, D-66123 Saarbr{\"u}cken, Germany},
  NUMBER = {MPI-I-96-1-028},
  MONTH = {November},
  YEAR = {1996},
  ISSN = {0946-011X},
}