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PASTEC specifications


Unique identifier OMICS_19087
Alternative name PASTEClassifier
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 1.0
Stability Stable
Source code URL
Maintained Yes


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  • person_outline Hadi Quesneville <>

Publication for PASTEC

PASTEC in pipelines

PMCID: 5638112
PMID: 28390096
DOI: 10.1111/mec.14134

[…] using default settings. the consensus sequences were exported as fasta files and retained as a cottus reference library of repetitive elements. to classify putative transposons, we used the software pasteclassifier (v. 1.0; hoede et al., ). pasteclassifier searches for characteristic structural and functional features of tes, including long terminal repeats (ltr), terminal inverted repeats […]

PMCID: 4641428
PMID: 26556056
DOI: 10.1186/s12864-015-2185-x

[…] cc148 [] at the expected location of an orf1 of a line retrotransposon, together with 3000 bp flanking sequence on each side. we obtained 34 extended te genome fragments that we annotated using pastec teclassifier []., we searched for eka te families using avra10 (gi|111035036|gb|dq679913| blumeria graminis f. sp. hordei isolate cc148 avra10 mrna, complete cds) and avrk1 […]

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PASTEC in publications

PMCID: 5886536
PMID: 29621340
DOI: 10.1371/journal.pone.0195461

[…] nucleotide or protein sequence if it had an alignment (blastn or blastx) covering 80% of the sequence for a nucleotide alignment, or had an evalue less than 1e-10 for a protein alignment., the tool (pastec) from repet version 2.2 [] provided further information for repeat classification. the annotation information, for all sequences flagged as potentially chimeric […]

PMCID: 5905499
PMID: 29253216
DOI: 10.1093/gigascience/gix125

[…] consensus models of putative interspersed repeats. a complementary analysis intended to augment the number of te sequences classified according to current criteria [] was performed using the pastec program []. repeatmasker open-4.0 (repeatmasker, rrid:scr_012954) [] was used with the sequences from the de novo repetitive element library to annotate the interspersed repeats and to detect […]

PMCID: 5689174
PMID: 29145801
DOI: 10.1186/s12864-017-4243-z

[…] s7.3 v2.0 (id: serlas7_3_2), pisolithus tinctorius marx 270 v1.0 (id: pisti1). briefly, de novo te detection was carried out with the tedenovo pipeline [] and the elements were classified with pastec []. the resulting te library was fed into teannot pipeline [] in two consecutive iterations: the first one with the full library, and the second with an improved library consisting […]

PMCID: 5644144
PMID: 29041914
DOI: 10.1186/s12864-017-4197-1

[…] assembly was achieved after sequence redundancy was removed using cd-hit (v3.1.1) [] with a 95% identity threshold., we searched for and classified repeats using repeatmodeler (v1.0.8) [] and pasteclassifier (v1.0) []. the program repeatmasker (v4.0.5) [] was used to mask the genome assembly prior to annotation for protein coding genes. we performed structural gene annotation with maker2 […]

PMCID: 5465968
PMID: 28594822
DOI: 10.1371/journal.pgen.1006777

[…] using recon [], grouper [] and piler []. the predictions from ltrharvest were clustered using the mcl algorithm. the consensus for each cluster are obtained using map [] and classified with pastec classifier []. the unclassified consensus sequences (nocat) were filtered out to keep only consensus sequences built from at least 10 sequences in the cluster. the library of 10,535 consensus […]

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PASTEC institution(s)
INRA, UR1164 URGI - Research Unit in Genomics-Info, Versailles, France; INRA, plateforme Bio-informatique Genotoul, Mathematiques et Informatique Appliquees Toulouse, Castanet-Tolosan, France; INRA, LUNAM Universite, Oniris, UMR1300 BioEpAR, Nantes, France
PASTEC funding source(s)
Supported by a grant from the French National Research. Agency (ANR-08-KBBE-012-02).

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