FootPrinter protocols

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Popular tool citations

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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 pipeline

2017
PMCID: 5333389
PMID: 28249564
DOI: 10.1186/s12859-017-1495-1

[…] due to next generation sequencing and the resulting avalanche of data [–]., examples for highly popular phylogenetic footprinting tools that have been applied to eukaryotes and prokaryotes are footprinter [], phyme [], monkey [], microfootprinter [], phylogenetic gibbs sampler [], phylogibbs [], phylogibbs-mp [], or motevo []., in summary, one-species approaches neglect phylogenetic […]


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FootPrinter in publications

 (23)
PMCID: 5333389
PMID: 28249564
DOI: 10.1186/s12859-017-1495-1

[…] due to next generation sequencing and the resulting avalanche of data [–]., examples for highly popular phylogenetic footprinting tools that have been applied to eukaryotes and prokaryotes are footprinter [], phyme [], monkey [], microfootprinter [], phylogenetic gibbs sampler [], phylogibbs [], phylogibbs-mp [], or motevo []., in summary, one-species approaches neglect phylogenetic […]

PMCID: 5447242
PMID: 28130227
DOI: 10.1093/bioinformatics/btx033

[…] resources, approaches for de-novo motif discovery based on phylogenetic footprinting have become increasingly attractive. examples of highly popular tools for phylogenetic footprinting are footprinter (), phyme (), monkey (), phylogibbs (), phylogenetic gibbs sampler (), phylogibbs-mp () and motevo (). provides a comparison of these tools regarding the used evolutionary model, […]

PMCID: 5014158
PMID: 27436282
DOI: 10.1093/jxb/erw275

[…] these methods can be categorized into three major classes: (1) methods based on position weight matrix (pwm), e.g. trap (), match (), and signal scan (); (2) phylogenetic footprinting methods, e.g. footprinter (), phyloscan (), and phyme (); and (3) standard motif-finding algorithms, e.g. gibbs sampling (), meme (), alignace (), ymf (), and weeder (). it is a common practice to combine […]

PMCID: 4263434
PMID: 25501842
DOI: 10.1371/journal.pone.0106033

[…] cheng kung university)., since only 1.3-kb upstream regulatory sequence of pemads3 was cloned, we then chose the 1.3-kb upstream sequences of pemads2∼5 for phylogenetic footprinting analysis by footprinter . this tool takes into account the evolutionary relationships and the phylogenetic tree analysis. the prediction of a conserved 10-bp or 11-bp motif with a 0-bp mutation allowance […]

PMCID: 3998923
PMID: 24762775
DOI: 10.1371/journal.pntd.0002823

[…] in culex quinquefasciatus, aedes aegypti and anopheles gambiae mosquitoes were then aligned and conserved transcription factor binding sites were identified using phylogenetic footprinting (footprinter2.0) . the results indicated that nf-κb (rel) (caccttcccc) and gata-1 (ttatcttt) transcription factor binding sites are conserved in the vago promoter region of the three mosquito species […]


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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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