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Protocols

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 citations

 (25)
call_split

Whole genome re sequencing of two Italian tomato landraces reveals sequence variations in genes associated with stress tolerance, fruit quality and long shelf life traits

2017
PMCID: 5909465
PMID: 29149280
DOI: 10.1093/dnares/dsx045
call_split See protocol

[…] 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 genomethreader 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 […]

library_books

A Transcriptome Survey Spanning Life Stages and Sexes of the Harlequin Bug, Murgantia histrionica

2017
PMCID: 5492069
PMID: 28587099
DOI: 10.3390/insects8020055

[…] using the method of le and gascuel [] as implemented in phyml [] using 100 bootstrap replicates. phylogenies were visually rendered using the r package, phytools []. for both gene family analyses, genomethreader [] was used to align m. histrionica proteins to the brown marmorated stink bug genome (available at https://i5k.nal.usda.gov/halyomorpha_halys) in an effort to elucidate patterns […]

library_books

Transcriptome sequencing reveals high isoform diversity in the ant Formica exsecta

2017
PMCID: 5701548
PMID: 29177112
DOI: 10.7717/peerj.3998

[…] by annotation evidence may exclude genes with very high divergent sequence evolution, and hence possibly some orphan genes ()., evidence-ta contigs were aligned to the genome of c. floridanus using genomethreader () to obtain information on gene structures (number and location of exons) of assembled transcripts, and to estimate the total number of genes and isoforms included in the evidence-ta. […]

library_books

Globally distributed root endophyte Phialocephala subalpina links pathogenic and saprophytic lifestyles

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

[…] and used as training dataset for augustus []. ab-initio gene prediction was performed on the masked genome using genemark-es [], augustus [] and fgenesh (neurospora and ustilago matrices). genomethreader [] was used to calculate spliced alignments for p. subalpina ests and protein data from related fungal species. the program was run based on a p. subalpina specific splicing model […]

library_books

A frameshift mutation in GON4L is associated with proportionate dwarfism in Fleckvieh cattle

2016
PMCID: 4818447
PMID: 27036302
DOI: 10.1186/s12711-016-0207-z

[…] of gon4l (ensbtag00000020356) based on the university of maryland (umd3.1) bovine genome sequence assembly [] and the dana-farber cancer institute bovine gene index release 12.0 [] using the genomethreader software tool []. the genomethreader output was viewed and edited using the apollo sequence annotation editor []., pcr primers were designed to analyze the polymorphism of rs723240647 […]

library_books

Homozygous haplotype deficiency reveals deleterious mutations compromising reproductive and rearing success in cattle

2015
PMCID: 4403906
PMID: 25927203
DOI: 10.1186/s12864-015-1483-7

[…] genomic structure of bovine slc2a2 was predicted based on the umd3.1 assembly of the bovine genome sequences [] and the dana-farber cancer institute bovine gene index release 12.0 [] by using the genomethreader software tool []. the genomethreader output was viewed and edited using the apollo sequence annotation editor []. the protein topology of bovine glut2 was predicted using the protter […]


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

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