TargetOrtho protocols

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TargetOrtho specifications

Information


Unique identifier OMICS_13080
Name TargetOrtho
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data Gene motifs and genes
Input format TXT, PWM
Output data Top-ranked site per gene, predicted binding sites in standard genome browsers
Output format HTML, TXT, BED
Operating system Unix/Linux
Programming languages C++, Python
License MIT License
Computer skills Advanced
Stability Stable
Requirements
MEME, scipy, numpy, matplotlib
Source code URL https://codeload.github.com/loriglenwinkel/TargetOrtho/zip/master
Maintained Yes

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Maintainer


  • person_outline Oliver Hobert <>

Publication for TargetOrtho

TargetOrtho in pipeline

2016
PMCID: 4866721
PMID: 27176626
DOI: 10.1371/journal.pgen.1006048

[…] []., ap-2 has been shown to bind to the palindromic consensus sequence 5'-gccn3ggc-3', as well as the binding motif 5'-gccn3/4ggg-3' []. we used either the 9bp or 10bp motif as an input for targetortho []. from the program output we selected only putative targets that are conserved in at least 4 caenoharbditis species, and are located within the 3 kb region upstream of the start codon. […]


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TargetOrtho in publications

 (2)
PMCID: 5908064
PMID: 29672507
DOI: 10.1371/journal.pbio.2004979

[…] length was set to k = 6 and the sequence search space was confined to 2-kb upstream regions. the discovered cacctg motif had a robustness score of 10/10 with a significance z-score of 18.3., we used targetortho [] to find whole genome cacctg motif matches in five nematode genomes searching 2 kb upstream of each gene plus introns. adl-expressed genes and all c. elegans genes, excluding noncoding […]

PMCID: 4866721
PMID: 27176626
DOI: 10.1371/journal.pgen.1006048

[…] however, this phenotype was never observed in the partial loss of function allele qm27. neither was it observed in aptf-2(rnai) nor following injection of aptf-2 dsrna into aptf-2(qm27)., using targetortho [], a phylogenetic footprinting tool to identify transcription factor targets, we identified within the c. elegans genome 1631 putative ap-2 tf binding sites in the 3kb upstream promoter […]


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TargetOrtho institution(s)
Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University Medical Center, New York, NY, USA
TargetOrtho funding source(s)
National Institutes of Health (R01NS039996-05, R01NS050266-03, 5T32DK007328-33)

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