Name
Abstract | ||
|---|---|---|
In this paper we describe some utilizing conditions of a recently published tool that offers two basic functions for the classical problem of discovering motifs in a set of promoter sequences. For the first it is assumed that not necessarily all of the sequences possess a common motif of given length l. In this case, CHECKPROMOTER allows an exact identification of maximal subsets of related promoters. The purpose of this program is to recognize putatively co-regulated genes. The second, CHECKMOTIF, solves the problem of checking if the given promoters have a common motif. It uses a fast approximation algorithm for which we were able to derive non-trivial low performance bounds (defined as the ratio of Hamming distance of the obtained solution to that of a theoretically best solution) for the computed outputs. Both programs use a novel weighted Hamming distance paradigm for evaluating the similarity of sets of l-mers, and we are able to compute performance bounds for the proposed motifs. A set of At promoters were used as a benchmark for a comparative test against five known tools. It could be verified that SiteSeeker significantly outperformed these tools. |
Year | DOI | Venue |
|---|---|---|
2009 | 10.3233/ISB-2009-0386 | in Silico Biology |
Keywords | DocType | Volume |
promoters,algorithms,genes | Journal | 9 |
Issue | ISSN | Citations |
1-2 | 1386-6338 | 0 |
PageRank | References | Authors |
0.34 | 6 | 3 |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Klaus Ecker | 1 | 41 | 9.16 |
| Jens Lichtenberg | 2 | 11 | 5.05 |
| Lonnie R. Welch | 3 | 314 | 45.64 |