 Structure of the transcriptional network controlling white-opaque switching in Candida albicans Mol Microbiol, 2013
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 Asexual populations of the human malaria parasite, Plasmodium falciparum, use a two-step genomic strategy to acquire accurate, beneficial DNA amplifications PLoS Pathog., 2013
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 PRICE: software for the targeted assembly of components of (Meta) genomic sequence data G3 (Bethesda), 2013
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 Identification and characterization of a previously undescribed family of sequence-specific DNA-binding domains PNAS, 2013
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 Microfluidic affinity and ChIP-seq analyses converge on a conserved FOXP2-binding motif in chimp and human, which enables the detection of evolutionarily novel targets Nucleic Acids Research, 2013
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 ACBD3 Interaction with TBC1 Domain 22 Protein Is Differentially Affected by Enteroviral and Kobuviral 3A Protein Binding mBio, 2013
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 Bartonella quintana Deploys Host and Vector Temperature-Specific Transcriptomes PLos One 2013
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|  Here we introduce HMMSplicer, an accurate and efficient algorithm for discovering canonical and non-canonical splice junctions in short read datasets. HMMSplicer identifies more splice junctions than currently available algorithms when tested on publicly available A. thaliana, P. falciparum, and H. sapiens datasets without a reduction in specificity. HMMSplicer was found to perform especially well in compact genomes and on genes with low expression levels, alternative splice isoforms, or non-canonical splice junctions. Because HHMSplicer does not rely on pre-built gene models, the products of inexact splicing are also detected. In addition, HMMSplicer provides a score for every predicted junction allowing the user to set a threshold to tune false positive rates depending on the needs of the experiment. HMMSplicer is implemented in Python. Code and documentation are freely available at the link below. Download HMMSplicer! (Updated Nov 25th 2010 - Version: 0.9.5) |
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