FootPrinter pipeline

FootPrinter specifications

Information


Unique identifier OMICS_25390
Name FootPrinter
Interface Web user interface
Restrictions to use None
Input data Some orthologous sequences and the phylogenetic tree related.
Output data A set of k-mers.
Computer skills Basic
Maintained No

Maintainer


This tool is not available anymore.

Publications for FootPrinter

FootPrinter IN pipelines

 (2)
2007
PMCID: 1803799
PMID: 17286865
DOI: 10.1186/1471-2105-8-46

[…] not conserved in the other species. finally, the conservation of functional sites often spans a region longer than the sites themselves, increasing the number of predicted nucleotides., we then ran footprinter also on this sequence set. again, the best performance (79% at the site level, 70% at the nucleotide level) was obtained by using a parsimony score threshold of 0 (no substitution allowed […]

2007
PMCID: 1803799
PMID: 17286865
DOI: 10.1186/1471-2105-8-46

[…] of the reference sequence, with 84% of success at the site level and 76% at the nucleotide level (see table 1). thus, with the same specificity, weederh yields a higher sensitivity. introducing for footprinter significance evaluation of motifs (using the different significance settings available and trying different combinations) did not improve the results, increasing the specificity but also […]

FootPrinter institution(s)
Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA
FootPrinter funding source(s)
Supported in part by a Natural Sciences and Engineering Research Council of Canada (NSERC) fellowship, by the National Science Foundation and DARPA under grant DBI-9601046, and by the National Science Foundation under grant DBI-9974498.

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