PASTEC statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Transposable element prediction chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

Protocols

To access compelling stats and trends, optimize your time and resources and pinpoint new correlations, you will need to subscribe to our premium service.

Subscribe

PASTEC specifications

Information


Unique identifier OMICS_19087
Name PASTEC
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 https://urgi.versailles.inra.fr/download/repet/PASTEClassifier-1.0.tar.gz
Maintained Yes

Versioning


Add your version

Maintainer


  • person_outline Hadi Quesneville <>

Publication for PASTEC

PASTEC in pipelines

 (2)
2017
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 […]

2015
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 […]


To access a full list of citations, you will need to upgrade to our premium service.

PASTEC in publications

 (15)
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 pasteclassifier.py 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 […]


To access a full list of publications, you will need to upgrade to our premium service.

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).

PASTEC reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review PASTEC