GenomeThreader pipeline

GenomeThreader specifications

Information


Unique identifier OMICS_07783
Name GenomeThreader
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Windows
Computer skills Advanced
Stability No
Maintained No

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Publication for GenomeThreader

GenomeThreader IN pipelines

 (3)
2017
PMCID: 5909465
PMID: 29149280
DOI: 10.1093/dnares/dsx045

[…] a download data section allows sequences and data to be accessed upon request. association of all the genes among the three genomes from each annotation (heinz 1706, cor and luc) was carried out by genomethreader36 using transcript to genome mapping of each landrace to the two alternative ones, with 95% and 85% of coverage and identity, respectively. this permitted to create crosslinks […]

2016
PMCID: 5148876
PMID: 27938347
DOI: 10.1186/s12864-016-3369-8

[…] the quality of the low identity genes (proteins with <30% identity with a protein sequence in simap) was assessed by mapping the protein sequences against the assembled 454 est dataset using genomethreader and analyzing the coverage of the gene model by ests. in addition, rna-seq data was available following the genome sequencing/annotation [108] […]

2014
PMCID: 3922800
PMID: 24490620
DOI: 10.1186/1471-2229-14-39

[…] and annotations (jgi v1.0) were retrieved from the citrus genome database (http://www.citrusgenomedb.org/)., gst encoding transcripts were aligned to the reference c. sinensis genome scaffolds using genomethreader [58] with 80% minimal nucleotide coverage and 80% sequence identity., all tissues/organs were taken and frozen in liquid nitrogen. the trizol® ls reagent (invitrogen, scotland uk) […]

GenomeThreader institution(s)
Zentrum für Bioinformatik, Universität Hamburg, Hamburg, Germany

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