EuGene-PP specifications


Unique identifier OMICS_04224
Name EuGene-PP
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data EuGene-PP can run using just FASTA genomic sequences and expression data (provided as oriented Single/Pair-end reads in either FASTQ/FASTA format, mapped reads in Bam/Sam, Bed or Wig format, or tiling array data in ndf/pair files).
Operating system Unix/Linux
Computer skills Advanced
Version 1.1
Stability Stable
Maintained Yes


No version available

Publication for EuGene-PP

EuGene-PP citations


Xanthomonas adaptation to common bean is associated with horizontal transfers of genes encoding TAL effectors

BMC Genomics
PMCID: 5577687
PMID: 28854875
DOI: 10.1186/s12864-017-4087-6

[…] strain to achieve ~100× coverage. De novo assembling was performed using HGAP assembler [] version 3.0 (Pacific Biosciences, Menlo Park, CA). Annotation of whole genome assemblies was performed with EuGene-PP version 1.2 automated pipeline [], using SWISS-PROT as protein and training protein databases ( The sequences of tal genes were manually retrieved using BLASTN searc […]


Comparative Genomics of Pathogenic and Nonpathogenic Strains of Xanthomonas arboricola Unveil Molecular and Evolutionary Events Linked to Pathoadaptation

Front Plant Sci
PMCID: 4686621
PMID: 26734033
DOI: 10.3389/fpls.2015.01126
call_split See protocol

[…] APdenovo 1.05 (Li et al., ) and Velvet 1.2.02 (Zerbino and Birney, ). Then contigs were scaffolded with LYNX (Gouzy, unpublished data) using mate-pair read information. Annotation was performed using EuGene-PP using similarities with known protein sequences (Sallet et al., ). A probably non-exhaustive list of known T3Es that were previously identified in various pathogenic bacteria genus (Xanthomo […]

EuGene-PP institution(s)
Laboratoire Interactions Plantes Micro-organismes (LIPM) UMR441/2594, INRA/CNRS, France; INRA, Unité de Mathématiques et Informatique Appliques de Toulouse, UR 875, Castanet-Tolosan, France
EuGene-PP funding source(s)
This work was supported by the Agence Nationale de la Recherche ANR-08-GENO-106 grant ‘SYMbiMICS’, in TULIP LabEx (ANR-10-LABX-41).

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