GenomeThreader protocols

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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

 (5)
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 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 […]

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 [] […]

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 [] 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) […]

2013
PMCID: 3729371
PMID: 23879659
DOI: 10.1186/1471-2164-14-498

[…] for the training and predictions. as additional evidence, homologous protein sequences (swissprot rel. 13.4 and arabidopsis thaliana tair7 [] homologs) and in particular est alignments 360,974 from genomethreader [], 118,243 from sim4 [] and 97,373 from exonerate [] were used. if available, we also provided est mate pair information into eugène (63,945 est mate pairs). two whole genome eugène […]

2012
PMCID: 3434094
PMID: 22559219
DOI: 10.1186/1471-2164-13-166

[…] a normalized est library of strain uamh 11012 sequenced on the 454 platform at fgcz (rémy bruggmann, unpublished). single 454 cdna reads belonging to the mt genome were filtered using the software genomethreader[] and the sequence coverage for each base in the mt genome was calculated (= number of reads covering a specific base in the genome)., a region between cox1 and nad1 included […]


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GenomeThreader in publications

 (23)
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 […]

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. […]

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 […]

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 […]

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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