Motif Libraries
The libraries offered here are formatted for import into MochiView using the Import Motifs utility. (Some of the libraries are quite redundant, but they often offer different variations on the binding motif for each transcription factor.) To download the libraries just right-click the link and choose ‘Save Link as…‘ (for most browsers left-clicking will show the text file in your browser).
Yeast Libraries
Combined Libraries (1067 motifs)
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This file contains all of the motifs from the individual yeast libraries presented below. Please be aware that there is considerable motif redundancy (or even exact duplication in the case of the JASPAR library, which contains motifs from some of the lists below).
JASPAR Library (177 motifs)
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This library contains the S. cerevisiae motifs found in the JASPAR database. This library is a curated collection of motifs, and is likely to be somewhat redundant with the other libraries provided below (reference#1 / reference#2 / reference#3 /motif_references / website).
SwissRegulon Library (80 motifs)
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This library of S. cerevisiae motifs is provided courtesy of Mikhail Pachkov of the SwissRegulon database (reference / website).
Gasch/Eisen Library (116 motifs)
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This library of ascomycete motifs is provided courtesy of Audrey Gasch and was produced during her time in the Eisen laboratory (reference / website).
Badis/Hughes Library (114 motifs)
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This library of S. cerevisiae motifs is provided courtesy of Tim Hughes and was produced by Badis et al. (reference).
MotifVoter Library (82 motifs)
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This library of S. cerevisiae motifs (and a few mammalian motifs) is provided courtesy of Edward Wijaya and the MotifVoter algorithm (reference / website).
MacIsaac Libraries (102/124 motifs)
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These libraries of S. cerevisiae motifs are provided courtesy of Kenzie MacIsaac. The first library comes from the 2004 Harbison et al. manuscript (Transcriptional regulatory code of a eukaryotic genome / source). The second, more recent, library comes from the 2006 MacIsaac et al. mansucript (An Improved Map of Conserved Regulatory Sites for Saccharomyces cerevisiae / source).
Zhu Library (89 motifs)
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This library of S. cerevisiae motifs was created by Zhu et al. and is described in the article High-resolution DNA-binding specificity analysis of yeast transcription factors. The data can also be found in the UniPROBE database.
Mouse Libraries
JASPAR Library (428 motifs)
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This library contains the M. musculus motifs found in the JASPAR database. This library is a curated collection of motifs, and is likely to be somewhat redundant with the other libraries provided below (reference#1 / reference#2 / reference#3 /motif_references / website).
Badis Library (208 motifs)
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This library of mouse motifs was created by Badis et al. and is described in the article Diversity and Complexity in DNA Recognition by Transcription Factors. The data can also be found in the UniPROBE database.
Berger Library (183 motifs)
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This library of mouse motifs was created by Berger et al. and is described in the article Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. (This library also contains three motifs from other species from the 2006 Berger et al. article: Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities.) The data can also be found in the UniPROBE database.
Human Library
JASPAR Library (318 motifs)
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This library contains the H. sapiens motifs found in the JASPAR database (reference#1 / reference#2 / reference#3 / motif_references / website).
Nematode Library
JASPAR Library (24 motifs)
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This library contains the C. elegans motifs found in the JASPAR database (reference#1 / reference#2 / reference#3 / motif_references / website).
Drosophila Library
JASPAR Library (128 motifs)
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This library contains the D. melanogaster motifs found in the JASPAR database (reference#1 / reference#2 / reference#3 / motif_references / website).
Multi-Species Library
JASPAR Library (1,316 motifs)
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This library contains all of the motifs found in the JASPAR database (reference#1 /reference#2 / reference#3 / motif_references / website).