Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
Suffix arrays: a new method for on-line string searches
SODA '90 Proceedings of the first annual ACM-SIAM symposium on Discrete algorithms
Reducing the space requirement of suffix trees
Software—Practice & Experience
Linear-Time Longest-Common-Prefix Computation in Suffix Arrays and Its Applications
CPM '01 Proceedings of the 12th Annual Symposium on Combinatorial Pattern Matching
Engineering a scalable placement heuristic for DNA probe arrays
RECOMB '03 Proceedings of the seventh annual international conference on Research in computational molecular biology
Rapid Large-Scale Oligonucleotide Selection for Microarrays
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
Computing Highly Specific and Mismatch Tolerant Oligomers Efficiently
CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
Fast and Sensitive Probe Selection for DNA Chips Using Jumps in Matching Statistics
CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
Efficient discovery of unique signatures on whole-genome EST databases
Proceedings of the 2005 ACM symposium on Applied computing
Integer linear programming approaches for non-unique probe selection
Discrete Applied Mathematics
Note: On the complexity of non-unique probe selection
Theoretical Computer Science
Probe Selection with Fault Tolerance
ICIC '08 Proceedings of the 4th international conference on Intelligent Computing: Advanced Intelligent Computing Theories and Applications - with Aspects of Theoretical and Methodological Issues
Efficient selection of unique and popular oligos for large EST databases
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
An efficient algorithm for finding gene-specific probes for DNA microarrays
ISBRA'07 Proceedings of the 3rd international conference on Bioinformatics research and applications
A fast preprocessing algorithm to select gene-specific probes of DNA microarrays
FAW'07 Proceedings of the 1st annual international conference on Frontiers in algorithmics
Independent component analysis algorithms for microarray data analysis
Intelligent Data Analysis - Knowledge Discovery in Bioinformatics
| Hi-index | 0.00 |
We present the first algorithm that selects oligonucleotide probes (e.g. 25-mers) for microarray experiments on a large scale. For example, oligos for human genes can be found within 50 hours. This becomes possible by using the longest common substring as a specificity measurefor candidate oligos. We present an algorithm based on a suffix array with additional information that is efficient both in terms of memory usage and running time to rank all candidate oligos according to their specificity. We also introduce the concept of master sequences to describe the sequences from which oligos are to be selected. Constraints such as oligo length, melting temperature, and self-complementarity are incorporated in the master sequence at a preprocessing stage and thus kept separate from the main selection problem. As a result, custom oligos can now be designed for any sequenced genome, just as the technology for on-site chip synthesis is becoming increasingly mature.