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PseudoPipe specifications


Unique identifier OMICS_20787
Name PseudoPipe
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data A genomic sequence after repeat-masking, A comprehensive and non-redundant set of protein sequences in the genome, A chromosomal coordinates of the functional genes.
Input format FASTA
Output data A complete annotation of the pseudogenes in the studied genome.
Output format TXT
Operating system Unix/Linux
Programming languages Python
License Apache License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes




No version available


  • person_outline Zhaolei Zhang
  • person_outline Mark Gerstein

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Publications for PseudoPipe

PseudoPipe citations


The Gastrodia elata genome provides insights into plant adaptation to heterotrophy

Nat Commun
PMCID: 5915607
PMID: 29691383
DOI: 10.1038/s41467-018-03423-5

[…] 8,969 true genes were masked. The BLAST hits were conjoined by Solar software. GeneWise was used to predict the pseudogene structures with the ‘-pseudo’ parameter. Pseudogenes were then classified by PseudoPipe. The PseudoPipe program applies a set of sequence identity and completeness cut-off to report a final set of good-quality pseudogene sequences. We used the following cutoffs: amino acid (AA […]


Neuronal expressed microRNA targeted pseudogenes compete with coding genes in the human brain

PMCID: 5611730
PMID: 28786976
DOI: 10.1038/tp.2017.163
call_split See protocol

[…] ing the data of the 1000 genomes project, which includes low coverage genotyping data of more than 2500 individuals of known ethnic origins. ( PSGs were identified by the PseudoPipe algorithm on the most updated genome build GRCh38.The MicroT algorithm (DIANA lab; predicts miRNA-binding sites described previously by Maragkakis et al. Br […]


Protein Coding Genes’ Retrocopies and Their Functions

PMCID: 5408686
PMID: 28406439
DOI: 10.3390/v9040080

[…] on and single-exon gene models to be obtained. These single-exon annotations are interpreted as intronless, and therefore possibly retrotransposed, gene copies []. A similar method was applied in the PseudoPipe pipeline to predict all types of pseudogenes in the eukaryotic genomes stored on the server []. A slightly different approach was applied in UCSC Genome Browser, which beside […]


Pseudogenes and Their Genome Wide Prediction in Plants

Int J Mol Sci
PMCID: 5187791
PMID: 27916797
DOI: 10.3390/ijms17121991

[…] nd the latter is accomplished through FASTA [], Prot_map [] or GeneWise [] algorithms to achieve a refined global alignment that shows positions of disablement (). For this purpose, pipelines such as PseudoPipe [], Shiu’s pipeline [] and PSF [] have been developed. […]


Computational Identification of Novel Genes: Current and Future Perspectives

Bioinform Biol Insights
PMCID: 4970615
PMID: 27493475
DOI: 10.4137/BBI.S39950

[…] y the existence of a pseudogene. Pseudogenes can be detected by homology of putative novel genes on the DNA level and might be compared to a database of collected pseudogenes like The PseudoPipe pipeline predicts pseudogenes in the genome using Blast and a clustering algorithm, but is limited to mammalian genomes. Alternatively, the classification might be baffled when the observed […]


Global Intersection of Long Non Coding RNAs with Processed and Unprocessed Pseudogenes in the Human Genome

Front Genet
PMCID: 4805607
PMID: 27047535
DOI: 10.3389/fgene.2016.00026

[…] verlap of the several currently available public pseudogene collections had not yet been performed. The GENCODE pseudogene resource (psiDR) is itself an integration of pseudogene annotation data from Pseudopipe, retroFinder, HaVANA, ENCODE, and the 1000 Genomes Project (Pei et al., ). This resource provides a high confidence but fairly exclusive dataset which utilizes manual annotation, computatio […]

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PseudoPipe institution(s)
Banting and Best Department of Medical Research, Donnelly CCBR, University of Toronto, Toronto, ON, Canada; Department of Computer Science, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, New Haven, CT, USA; Department of Biology, Pennsylvania State University, University Park, PA, USA ; Department of Biology, McGill University, Stewart Biology Building, Montreal, QC, Canada
PseudoPipe funding source(s)
Supported by University of Toronto Faculty of Medicine; and the NIH/NHGRI (IU01HG003156-01).

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