Showing papers by "Hans-Peter Lenhof published in 1998"
TL;DR: This paper addresses the problem of optimally aligning a given RNA sequence of unknown structure to one of known sequence and structure using methods from polyhedral combinatorics and could solve large problem instances--23S ribosomal RNA with more than 1400 bases.
Abstract: Ribonucleic acid (RNA) is a polymer composed of four bases denoted A, C, G, and U. It generally is a single-stranded molecule where the bases form hydrogen bonds within the same molecule leading to structure formation. In comparing different homologous RNA molecules it is important to consider both the base sequence and the structure of the molecules. Traditional alignment algorithms can only account for the sequence of bases, but not for the base pairings. Considering the structure leads to significant computational problems because of the dependencies introduced by the base pairings. In this paper we address the problem of optimally aligning a given RNA sequence of unknown structure to one of known sequence and structure. We phrase the problem as an integer linear program and then solve it using methods from polyhedral combinatorics. In our computational experiments we could solve large problem instances--23S ribosomal RNA with more than 1400 bases--a size intractable for former algorithms.
72 citations
01 Mar 1998
TL;DR: This paper addresses the problem of optimally aligning a given RNA sequence of unknown structure to one of known sequence and structure by phrase the problem as an integer linear program and then solve it using methods from polyhedral combinatorics.
Abstract: Ribonucleic acid (RNA) is a polymer composed of four bases denoted A, C, G, and U. It generally is a single-stranded molecule where the bases form hydrogen bonds within the same molecule leading to structure formation. In comparing different homologous RNA molecules it is important to consider both the base sequence and the structure of the molecules. Traditional alignment algorithms can only account for the sequence of bases, but not for the base pairings. Considering the structure leads to significant computational problems because of the dependencies introduced by the base pairings. In this paper we address the problem of optimally aligning a given RNA sequence of unknown structure to one of known sequence and structure. We phrase the problem as an integer linear program and then solve it using methods from polyhedral combinatorics. In our computational experiments we could solve large problem instances—23S ribosomal RNA with more than 1400 bases—a size intractable for former algorithms.
52 citations
01 Jan 1998
2 citations
01 Jan 1998
TL;DR: In this article, the problem of optimally aligning a given RNA sequence of unknown structure to one of known sequence and structure was formulated as an integer linear program and then solved using methods from polyhedral combinatorics.
Abstract: Ribonucleic acid (RNA) is a polymer composed of four bases denoted A, C, G, and U It generally is a single-stranded molecule where the bases form hydrogen bonds within the same molecule leading to structure formation In comparing different homologous RNA molecules it is important to consider both the base sequence and the structure of the molecules Traditional alignment algorithms can only account for the sequence of bases, but not for the base pairings Considering the structure leads to significant computational problems because of the dependencies introduced by the base pairings In this paper we address the problem of optimally aligning a given RNA sequence of unknown structure to one of known sequence and structure We phrase the problem as an integer linear program and then solve it using methods from polyhedral combinatorics In our computational experiments we could solve large problem instances--23S ribosomal RNA with more than 1400 bases--a size intractable for former algorithms