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» ASPIC: a novel method to predict the exon-intron structure o...
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BMCBI
2005
122views more  BMCBI 2005»
13 years 4 months ago
ASPIC: a novel method to predict the exon-intron structure of a gene that is optimally compatible to a set of transcript sequenc
Background: Currently available methods to predict splice sites are mainly based on the independent and progressive alignment of transcript data (mostly ESTs) to the genomic seque...
Paola Bonizzoni, Raffaella Rizzi, Graziano Pesole
ALMOB
2006
155views more  ALMOB 2006»
13 years 4 months ago
A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons
Background: An important challenge in eukaryotic gene prediction is accurate identification of alternatively spliced exons. Functional transcripts can go undetected in gene expres...
Jonathan E. Allen, Steven L. Salzberg
RECOMB
2005
Springer
14 years 5 months ago
Predicting Transcription Factor Binding Sites Using Structural Knowledge
Abstract. Current approaches for identification and detection of transcription factor binding sites rely on an extensive set of known target genes. Here we describe a novel structu...
Tommy Kaplan, Nir Friedman, Hanah Margalit
BMCBI
2006
116views more  BMCBI 2006»
13 years 4 months ago
Optimized mixed Markov models for motif identification
Background: Identifying functional elements, such as transcriptional factor binding sites, is a fundamental step in reconstructing gene regulatory networks and remains a challengi...
Weichun Huang, David M. Umbach, Uwe Ohler, Leping ...
BMCBI
2008
118views more  BMCBI 2008»
13 years 4 months ago
MetWAMer: eukaryotic translation initiation site prediction
Background: Translation initiation site (TIS) identification is an important aspect of the gene annotation process, requisite for the accurate delineation of protein sequences fro...
Michael E. Sparks, Volker Brendel