MicroFootPrinter protocols

View MicroFootPrinter computational protocol

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MicroFootPrinter specifications

Information


Unique identifier OMICS_24484
Name MicroFootPrinter
Software type Application/Script
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Martin Tompa <>

Publication for MicroFootPrinter

MicroFootPrinter in pipelines

 (2)
2017
PMCID: 5333389
PMID: 28249564
DOI: 10.1186/s12859-017-1495-1

[…] 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 information, whereas phylogenetic […]

2016
PMCID: 4977642
PMID: 27507169
DOI: 10.1186/s12864-016-2982-x

[…] to conduct performance comparison, we applied six de novo motif finding tools previously mentioned, i.e., biprospector, consensus, mdscan, meme, cubic, bobro and a phylogenetic footprinting pipeline microfootprinter [–, , , , ] on the same genome and compared with mp3. we followed tompa’s method [] and assessed the predictions both at nucleotide level and at the binding site level. specifically, […]


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MicroFootPrinter in publications

 (3)
PMCID: 5333389
PMID: 28249564
DOI: 10.1186/s12859-017-1495-1

[…] 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 information, whereas phylogenetic […]

PMCID: 4977642
PMID: 27507169
DOI: 10.1186/s12864-016-2982-x

[…] to conduct performance comparison, we applied six de novo motif finding tools previously mentioned, i.e., biprospector, consensus, mdscan, meme, cubic, bobro and a phylogenetic footprinting pipeline microfootprinter [–, , , , ] on the same genome and compared with mp3. we followed tompa’s method [] and assessed the predictions both at nucleotide level and at the binding site level. specifically, […]

PMCID: 1913097
PMID: 17616982
DOI: 10.1371/journal.pcbi.0030126

[…] immediately upstream of the selected gene. to handle this complication in a conservative manner, we extracted the noncoding sequences upstream of the gene and upstream of its plausible operon using microfootprinter []. specifically, if the next coding region upstream is in the same orientation and fewer than 100 nucleotides upstream, this short intergenic sequence is included in our sequence […]


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MicroFootPrinter institution(s)
Department of Computer Science and Engineering and Department of Genome Sciences, University of Washington, Seattle, WA, USA
MicroFootPrinter funding source(s)
Supported by the National Science Foundation under grant DBI-0218798 and by the National Institutes of Health under grant R01 HG02602.

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