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ICASSP
2007
IEEE
16 years 1 months ago
Fast Search of Sequences with Complex Symbol Correlations using Profile Context-Sensitive HMMS and Pre-Screening Filters
Recently, profile context-sensitive HMMs (profile-csHMMs) have been proposed which are very effective in modeling the common patterns and motifs in related symbol sequences. Pro...
Byung-Jun Yoon, P. P. Vaidyanathan
SPIRE
2007
Springer
16 years 26 days ago
Approximate String Matching with Lempel-Ziv Compressed Indexes
Abstract. A compressed full-text self-index for a text T is a data structure requiring reduced space and able of searching for patterns P in T. Furthermore, the structure can repro...
Luís M. S. Russo, Gonzalo Navarro, Arlindo ...
CIBCB
2006
IEEE
16 years 24 days ago
Motif Evaluation by Leave-one-out Scoring
Abstract— We propose a new method for collecting information on regulatory elements found by any motif discovery program. We suggest that combining the results of n leave-oneout ...
Audrey Girouard, Noah W. Smith, Donna K. Slonim
CIBCB
2006
IEEE
16 years 24 days ago
Machine Learning in Basecalling Decoding Trace Peak Behaviour
— DNA sequence basecalling is commonly regarded as a solved problem, despite significant error rates being reflected in inaccuracies in databases and genome annotations. These er...
David Thornley, Stavros Petridis
166
Voted
CIBCB
2006
IEEE
16 years 24 days ago
E2D: A Novel Tool for Annotating Protein Domains in Expressed Sequence Tags
The vast number of expressed sequence tags (ESTs) in public databases provides an important resource for comparative and functional genomics. A variety of methods based on homology...
Guo-Hsing Lee, Nai-Yu Chuang, Wen-Dar Lin, Chung-D...