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Gff2ps specifications

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Unique identifier OMICS_17140
Name Gff2ps
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data An annotated feature of a genomic sequence.
Input format GFF
Output format PostScript
Operating system Unix/Linux
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for Gff2ps

Gff2ps citations

 (6)
library_books

Relationship between Differential Hepatic microRNA Expression and Decreased Hepatic Cytochrome P450 3A Activity in Cirrhosis

2013
PMCID: 3772944
PMID: 24058572
DOI: 10.1371/journal.pone.0074471

[…] sites predicted by mirna were formatted into a general feature format (gff) file using the binding co-ordinates with respect to the utr regions, to visualize the location of the binding sites using gff2ps tool []., hepatic cyp3a activity in cirrhotic liver samples was significantly lower compared to normal liver tissue by 1.7-fold (0.28 ± 0.06 vs. 0.47 ± 0.07ml* min-1*mg protein-1 (mean ± sem), […]

library_books

Patterns of Sequence Divergence and Evolution of the S1 Orthologous Regions between Asian and African Cultivated Rice Species

2011
PMCID: 3053390
PMID: 21423767
DOI: 10.1371/journal.pone.0017726

[…] evaluated by alignment with rice est and full-length cdna (flcdna) public sequences . detailed analysis was performed with the emboss analysis software and the physical map diagram was drawn using gff2ps software . putative transposable elements (tes) were first identified and annotated by repeatmasker searches (http://www.repeatmasker.org) against local databases of rice tes downloaded […]

library_books

The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences

2010
PMCID: 2996948
PMID: 20609256
DOI: 10.1186/1471-2164-11-420

[…] groups: 70-84%, 85-97% and 98-100%. the genomic sampling was conducted 10 times and averaged., to simultaneously visualize all elements that were identified in the bac assemblies, the program gff2ps was used []. the following data were formatted into gff files and used to create figure and additional file , figure s1: maker dicot and monocot runs on masked and unmasked sequence; simple […]

library_books

Centromere sequence and dynamics in Dictyostelium discoideum

2009
PMCID: 2665215
PMID: 19179372
DOI: 10.1093/nar/gkp017

[…] trnascan () was used to search for trna genes. repeat positions were transformed to a gff file format for each centromere. a graphical representation of the centromeres was obtained using gff2ps () on these gff-files., from the blast analysis, we identified 34 full-length or nearly full-length dirs elements on all centromeres. these elements were aligned using clustalx (). […]

library_books

Conserved chromosomal clustering of genes governed by chromatin regulators in Drosophila

2008
PMCID: 2592712
PMID: 18783608
DOI: 10.1186/gb-2008-9-9-r134

[…] for the trx antibody. we thank f casares and m rehmsmeier for insightful discussions, and a carbonell for interesting suggestions. we are grateful to jf abril for helpful assistance with the program gff2ps, a coppe for introducing slight modifications in the reef program to identify small clusters and b lenhard for providing information about the genomic regulatory blocks in insects. we also […]

library_books

Multiple non collinear TF map alignments of promoter regions

2007
PMCID: 1878506
PMID: 17456238
DOI: 10.1186/1471-2105-8-138

[…] includes the score and the length of the optimal mma, and the matches in the input tf-maps (see figure for an example). a graphical representation of the mma is also displayed using the program gff2ps []., the optimal mma of a set of tf-maps is obviously dependant on the values of the α, λ, μ, γ and c parameters. in addition, the optimal parameter configuration is likely to depend […]


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Gff2ps institution(s)
Grup de Recerca en Informatica Medica, Institut Municipal d’Investigacio Medica (IMIM), Universitat Pompeu Fabra (UPF), Barcelona, Spain
Gff2ps funding source(s)
Supported by a grant from Plan Nacional de I+D, BIO98-0443-C02-01, and by a fellowship from the Instituto de Salud Carlos III, 99/9345.

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