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...le structural characteristics. Some other sequencebased methods use additional types of data to reduce the FPR of TFBS prediction, such as phylogenetic conservation (56), genome annotation [e.g. Refs =-=(57,58)-=-] or specific experimental results [e.g. Ref. (59)]. We only consider sequence-based methods not needing such additional information as methods comparable with ours. Some of these methods are SiteSleu...

Citation Context

...le structural characteristics. Some other sequencebased methods use additional types of data to reduce the FPR of TFBS prediction, such as phylogenetic conservation (56), genome annotation [e.g. Refs =-=(57,58)-=-] or specific experimental results [e.g. Ref. (59)]. We only consider sequence-based methods not needing such additional information as methods comparable with ours. Some of these methods are SiteSleu...

Citation Context

...le structural characteristics. Some other sequencebased methods use additional types of data to reduce the FPR of TFBS prediction, such as phylogenetic conservation (56), genome annotation [e.g. Refs =-=(57,58)-=-] or specific experimental results [e.g. Ref. (59)]. We only consider sequence-based methods not needing such additional information as methods comparable with ours. Some of these methods are SiteSleu...

Citation Context

...le structural characteristics. Some other sequencebased methods use additional types of data to reduce the FPR of TFBS prediction, such as phylogenetic conservation (56), genome annotation [e.g. Refs =-=(57,58)-=-] or specific experimental results [e.g. Ref. (59)]. We only consider sequence-based methods not needing such additional information as methods comparable with ours. Some of these methods are SiteSleu...

Citation Context

...le structural characteristics. Some other sequencebased methods use additional types of data to reduce the FPR of TFBS prediction, such as phylogenetic conservation (56), genome annotation [e.g. Refs =-=(57,58)-=-] or specific experimental results [e.g. Ref. (59)]. We only consider sequence-based methods not needing such additional information as methods comparable with ours. Some of these methods are SiteSleu...

Citation Context

...le structural characteristics. Some other sequencebased methods use additional types of data to reduce the FPR of TFBS prediction, such as phylogenetic conservation (56), genome annotation [e.g. Refs =-=(57,58)-=-] or specific experimental results [e.g. Ref. (59)]. We only consider sequence-based methods not needing such additional information as methods comparable with ours. Some of these methods are SiteSleu...

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...SS regions of genes. Kim et al. (21) introduced a Bayesian model to incorporate positional bias of transcription factor binding sites (TFBSs) in promoter regions to discover DNA motifs. Narang et al. =-=(22)-=- introduced a spatial confinement score combined with an over-representation score and relative entropy score to discover DNA motifs. Using positional preference for DNA motif discovery was most recen...

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...ate motifs. Other programs allow users to specify the prior distribution of position preference or sequence rank preference [6, 52] by adding a prior distribution component in their scoring functions =-=[89, 78, 36]-=-. However, the users may not know the correct prior(s) to begin with. Even worse, different motifs may have different preferences. For example, in ChIP-seq experiments, some motifs prefer to occur in ...

Citation Context

...SS regions of genes. Kim et al. (21) introduced a Bayesian model to incorporate positional bias of transcription factor binding sites (TFBSs) in promoter regions to discover DNA motifs. Narang et al. =-=(22)-=- introduced a spatial confinement score combined with an overrepresentation score and relative entropy score to discover DNA motifs. Using positional preference for DNA motif discovery was most recent...

Citation Context

...le structural characteristics. Some other sequencebased methods use additional types of data to reduce the FPR of TFBS prediction, such as phylogenetic conservation (56), genome annotation [e.g. Refs =-=(57,58)-=-] or specific experimental results [e.g. Ref. (59)]. We only consider sequence-based methods not needing such additional information as methods comparable with ours. Some of these methods are SiteSleu...