Summary
Discovery of transcription factor binding sites is a crucial and challenging problem in bioinformatics. Several computational tools have been developed for this problem, popularly known as the motif-finding problem. PhyME is an ab initio motif-finding algorithm, which finds overrepresented motifs in input sequences while accounting for their evolutionary conservation in orthologs of those sequences. Here, we describe the usage of this algorithm, publicly available as a Linux-based implementation.
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References
Sinha, S., Blanchette, M., and Tompa, M. (2004) PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences. BMC Bioinformatics 5, 170.
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© 2007 Humana Press Inc.
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Sinha, S. (2007). PhyME. In: Bergman, N.H. (eds) Comparative Genomics. Methods in Molecular Biology™, vol 395. Humana Press. https://doi.org/10.1007/978-1-59745-514-5_19
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DOI: https://doi.org/10.1007/978-1-59745-514-5_19
Publisher Name: Humana Press
Print ISBN: 978-1-58829-693-1
Online ISBN: 978-1-59745-514-5
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