Genie protocols

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Genie specifications

Information


Unique identifier OMICS_07795
Name Genie
Interface Web user interface
Restrictions to use None
Computer skills Basic
Maintained No

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This tool is not maintained anymore.

Publications for Genie

Genie in pipelines

 (2)
2015
PMCID: 4558851
PMID: 26201648
DOI: 10.1093/gbe/evv133

[…] available; 2) mapping of the available m. galloprovincialis sequencing reads (see above), with the clc genomics workbench “large gap mapping” tool; and 3) refinement of splice site positions with genie (). an example of the results of the annotation procedure is shown in supplementary figure s1, supplementary material online. results obtained from the genome and transcriptome analyses […]

2011
PMCID: 3356076
PMID: 22654816
DOI: 10.3389/fendo.2011.00059

[…] sequence was assembled, and the proctolin cdna sequence compared to the assembled sequence to predict the location and size of exons/introns. the splice site prediction was confirmed using genie (reese et al., ). rhopr-proctolin prepropeptide and its homologous sequences (a. pisum, acypig674496; d. melanogaster, np609158.2; t. castaneum, efa05689.1; litopenaeus vannamei, fe183480; d. […]


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Genie in publications

 (13)
PMCID: 5744146
PMID: 29207524
DOI: 10.3390/v9120371

[…] between ehadv 06-106 and bat adenovirus wiv17, as well as between ehadv 06-106 and bat adenovirus wiv18, were compared by global genome pairwise using mvista []. splice sites were predicted by the genie program []. distance matrix analysis of the dna polymerase (pol) amino acid sequence was performed by using mega 6.0 software., the animal cell lines vero e6 (monkey kidney), zfbk13-76e (e. […]

PMCID: 5642559
PMID: 29050284
DOI: 10.18632/oncotarget.19697

[…] heterozygous; hom, homozygous., several in silico analysis programs were used to predict the effect of the compound heterozygous mutations in oca2 (c.808-3c>g and c.2080-2a>g) on splicing. the genie program performs splice site score calculation. the results indicated that the mutants showed a remarkable decrease of the splice site score (table ). the netgene2 program showed that both oca2 […]

PMCID: 5172443
PMID: 15629048
DOI: 10.1016/S1672-0229(04)02014-5

[…] in the output sequence from the state need not to be identically and independently distributed., the ghmm model has been successfully implemented in gene finding programs, such as genscan and genie , and has been adopted by others for cross-species gene finding since the exon lengths are not geometrically distributed., it represents yet another variant to the standard hmm […]

PMCID: 4933364
PMID: 27379672
DOI: 10.1371/journal.pone.0157521

[…] from the genotype-tissue expression (gtex) database [], geuvadis [], and other recent studies [–] using haploreg and the gtex portal. further, we evaluated variants in potential splice sites using genie []., the relative strength of functional candidates was determined based on the accumulation of evidence from each of these datasets. a priori, we defined a score to summarize the amount […]

PMCID: 4558851
PMID: 26201648
DOI: 10.1093/gbe/evv133

[…] available; 2) mapping of the available m. galloprovincialis sequencing reads (see above), with the clc genomics workbench “large gap mapping” tool; and 3) refinement of splice site positions with genie (). an example of the results of the annotation procedure is shown in supplementary figure s1, supplementary material online. results obtained from the genome and transcriptome analyses […]


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Genie institution(s)
Human Genome Informatics Group, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Baskin Center for Computer Engineering and Computer Science, University of California, Santa Cruz, CA, USA
Genie funding source(s)
Supported by DOE grant no. DE-FG03-95ER62112 and DE-AC03-76SF00098, and the Aspen Center for Physics, Biosequence Analysis Workshop.

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