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- ArticleApril 2001
Fast and simple character classes and bounded gaps pattern matching, with application to protein searching
RECOMB '01: Proceedings of the fifth annual international conference on Computational biologyPages 231–240https://doi.org/10.1145/369133.369220The problem of fast searching of a pattern that contains Classes of characters and Bounded size Gaps (CBG) in a text has a wide range of applications, among which a very important one is protein pattern matching (for instance, one PROSITE protein site ...
- ArticleApril 2001
Optimal sequencing by hybridization in rounds
RECOMB '01: Proceedings of the fifth annual international conference on Computational biologyPages 141–148https://doi.org/10.1145/369133.369187Sequencing by hybridization (SBH) is a method for reconstructing a sequence over a small finite alphabet from a collection of probes (substrings). Substring queries can be arranged on an array (SBH chip) and then a combinatorial method is used to ...
- ArticleApril 2001
Algorithms for identifying protein cross-links via tandem mass spectrometry
RECOMB '01: Proceedings of the fifth annual international conference on Computational biologyPages 95–102https://doi.org/10.1145/369133.369177Cross-linking technology combined with tandem mass spectrometry (MS-MS) is a powerful method that provides a rapid solution to the discovery of protein-protein interactions and protein structures. We studied the problem of detecting cross-linked ...
- ArticleApril 2001
Gene-finding via tandem mass spectrometry
RECOMB '01: Proceedings of the fifth annual international conference on Computational biologyPages 87–94https://doi.org/10.1145/369133.369176We propose a new gene-finding methodology that combines high performance liquid chromatograph (HPLC)-tandem mass spectrometry experiments with a fast computer algorithm to locate coding regions and introns. Proteins are first extracted from cells and ...
- ArticleApril 2001
An optimal procedure for gap closing in whole genome shotgun sequencing
RECOMB '01: Proceedings of the fifth annual international conference on Computational biologyPages 22–30https://doi.org/10.1145/369133.369152Tettelin et. al. proposed a new method for closing the gaps in whole genome shotgun sequencing projects. The method uses a multiplex PCR strategy in order to minimize the time and effort required to sequence the DNA in the missing gaps. This procedure ...