Name
Abstract | ||
|---|---|---|
Fast and exact comparison of large genomic sequences remains a challenging task in biosequence analysis. We consider the problem of finding all epsilon-matches between two sequences, i.e., all local alignments over a given length with an error rate of at most epsilon. We study this problem theoretically, giving an efficient q-gram filter for solving it. Two applications of the filter are also discussed, in particular genomic sequence assembly and BLAST-like sequence comparison. Our results show that the method is 25 times faster than BLAST, while not being heuristic. |
Year | DOI | Venue |
|---|---|---|
2005 | 10.1089/cmb.2006.13.296 | JOURNAL OF COMPUTATIONAL BIOLOGY |
Keywords | DocType | Volume |
q-grams,filter,local alignment searching,sequence assembly,EST clustering | Conference | 13.0 |
Issue | ISSN | Citations |
2 | 1066-5277 | 42 |
PageRank | References | Authors |
5.14 | 12 | 3 |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Kim R. Rasmussen | 1 | 42 | 5.14 |
| Jens Stoye | 2 | 1341 | 134.73 |
| Eugene Myers | 3 | 3164 | 496.92 |