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Number of citations per year for the bioinformatics software tool PASTEC
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This map represents all the scientific publications referring to PASTEC per scientific context
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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


No version available

Maintainer


  • person_outline Hadi Quesneville

Publication for PASTEC

PASTEC citations

 (16)
library_books

Chinook salmon (Oncorhynchus tshawytscha) genome and transcriptome

2018
PLoS One
PMCID: 5886536
PMID: 29621340
DOI: 10.1371/journal.pone.0195461

[…] 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 by PASTEC, was manually reviewed. Where real chimeric sequences were verified (formed from the fusion of TEs from multiple taxa), the sequences were annotated as unknown. Otherwise, they were classified […]

library_books

Comparative genomics of Coniophora olivacea reveals different patterns of genome expansion in Boletales

2017
BMC Genomics
PMCID: 5689174
PMID: 29145801
DOI: 10.1186/s12864-017-4243-z

[…] rymans 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 on consensus […]

library_books

Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution

2017
BMC Genomics
PMCID: 5644144
PMID: 29041914
DOI: 10.1186/s12864-017-4197-1

[…] 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 ( […]

library_books

Linkage mapping aided by de novo genome and transcriptome assembly in Portunus trituberculatus: applications in growth related QTL and gene identification

2017
Sci Rep
PMCID: 5554138
PMID: 28801606
DOI: 10.1038/s41598-017-08256-8

[…] titive sequence database was built to predict repeat sequences. The software programs LTR_FINDER, MITE-Hunter, RepeatScout, and PILER-DF were used to construct a de novo repeat library, classified by PASTEClassifier, and combined with the Repbase transposable element library to act as the final library. The software Repeat-Masker was then run to find homologous repeats in the final library. Then, […]

library_books

Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant parasitic nematodes

2017
PLoS Genet
PMCID: 5465968
PMID: 28594822
DOI: 10.1371/journal.pgen.1006777

[…] clustered 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 s […]

library_books

Copy number increases of transposable elements and protein‐coding genes in an invasive fish of hybrid origin

2017
Mol Ecol
PMCID: 5638112
PMID: 28390096
DOI: 10.1111/mec.14134

[…] na resulted in a total of 7,548 sequences, which were assembled in seqman pro into 1,005 contigs (hereafter referred to as “repetitive elements”; size range: 500‐50k bp; n50: 2,978 bp; Table ). Using pasteclassifier, we classified 452 repetitive elements (45%) according to Wicker's classification system of TEs. These included 312 putative retrotransposons (Class I elements), 119 putative DNA trans […]


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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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