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PipMaker specifications

Information


Unique identifier OMICS_00944
Name PipMaker
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Two genomic sequences.
Input format FASTA
Output data A percent identity plot.
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Subtools


  • Laj
  • MultiPipTools
  • Tffind

Versioning


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Maintainer


  • person_outline PipMaker Team <>

Additional information


http://pipmaker.bx.psu.edu/pipmaker/

Information


Unique identifier OMICS_00944
Name PipMaker
Interface Web user interface
Restrictions to use None
Input data Two genomic sequences.
Input format FASTA
Output data A percent identity plot.
Computer skills Basic
Stability Stable
Maintained Yes

Subtools


  • Laj
  • MultiPipTools
  • Tffind

Maintainer


  • person_outline PipMaker Team <>

Additional information


http://pipmaker.bx.psu.edu/pipmaker/

Publications for PipMaker

PipMaker in publications

 (4)
PMCID: 4560928
PMID: 26341737
DOI: 10.1186/s13058-015-0636-6

[…] genes having at least one significant hit were kept, and for genes with multiple significant hits, only the best one is reported., the global mapping of the hoxc11 motif was performed using the tffind programme []. the hoxc11 motif frequency matrix (pfm) and representing logo were identified from the uniprobe database []. the first bp and the last 3 bp of this motif were deemed to have low […]

PMCID: 3894159
PMID: 24453983
DOI: 10.1371/journal.pgen.1004076

[…] were identified using the δct method, compared to the expression of act1., the upc2 binding site motif was downloaded from the jaspar database (http://jaspar.genereg.net/) and used as input for tffind (http://globin.cse.psu.edu/dist/tffind/) to scan promoter regions from each genome () using a cut off of 0.95 (95% confidence). a one-tailed fisher exact test was performed to compare […]

PMCID: 2883962
PMID: 20433755
DOI: 10.1186/1476-4598-9-98

[…] 7.0 of the transfac database [], using matrix ids 'v$nfkappab50_01' and 'v$nfkappab65_01', respectively. matches to each pwm were identified in promoter regions using a slightly modified version of tffind [], with default matrix similarity thresholds., chromatin immunoprecipitation (chip) reagents were purchased from upstate cell signaling (billerica, ma, usa). ht29 colon cancer cells (1 × 106) […]

PMCID: 1878502
PMID: 17477880
DOI: 10.1186/1752-0509-1-20

[…] base-pair regions of 14,368 genes were downloaded from the ucsc genome browser [] for the human genome (may 2004 build) []., a binding site score between a gene g and matrix m, bgm, is computed with tffind [], a program that assigns a score, ranging from 0 (very different from m) to 1 (perfect match to m), for each position in g's upstream region. bgm is defined as the highest position-specific […]

PipMaker institution(s)
The Pennsylvania State University, University Park, PA, USA
PipMaker funding source(s)
Supported by grant HG02238 from the National Human Genome Research Institute.

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