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Genie specifications

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

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Publications for Genie

Genie citations

 (11)
library_books

Characterization of a Novel Bat Adenovirus Isolated from Straw Colored Fruit Bat (Eidolon helvum)

2017
Viruses
PMCID: 5744146
PMID: 29207524
DOI: 10.3390/v9120371

[…] es 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. […]

library_books

Myticalins: A Novel Multigenic Family of Linear, Cationic Antimicrobial Peptides from Marine Mussels (Mytilus spp.)

2017
Mar Drugs
PMCID: 5577615
PMID: 28829401
DOI: 10.3390/md15080261

[…] were detected by TBLASTN against the mussel draft genome []. Exon and introns were detected by the alignment of assembled transcripts with genomic contigs and exon/intron junctions were refined with Genie [].Subsequently, the analysis was extended to other bivalve species, based on the dataset of transcriptomes described in [] and the available genomes, i.e., C. gigas [], Pinctada fucata [], Mizu […]

call_split

Mutational analysis of a Chinese family with oculocutaneous albinism type 2

2017
Oncotarget
PMCID: 5642559
PMID: 29050284
DOI: 10.18632/oncotarget.19697
call_split See protocol

[…] //wintervar.wglab.org/), MutationTaster (http://www.mutationtaster.org/), and Ensembl database (http://asia.ensembl.org/index.html) [, ]. To predict the splice site, the following programs were used: GENIE program (http://rulai.cshl.edu/new_alt_exon_db2/HTML/score.html), NNSPLICE (http://www.fruitfly.org/seq_tools/splice.html), and NetGene2 (http://www.cbs.dtu.dk/services/NetGene2/) [–]. […]

library_books

Fine Mapping of Common Genetic Variants Associated with Colorectal Tumor Risk Identified Potential Functional Variants

2016
PLoS One
PMCID: 4933364
PMID: 27379672
DOI: 10.1371/journal.pone.0157521

[…] es 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 of functi […]

call_split

Identification and Characterization of a Novel Family of Cysteine Rich Peptides (MgCRP I) from Mytilus galloprovincialis

2015
Genome Biol Evol
PMCID: 4558851
PMID: 26201648
DOI: 10.1093/gbe/evv133
call_split See protocol

[…] ver 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 were com […]

library_books

Isolation and Functional Characterization of Calcitonin Like Diuretic Hormone Receptors in Rhodnius prolixus

2013
PLoS One
PMCID: 3843727
PMID: 24312424
DOI: 10.1371/journal.pone.0082466

[…] The intron-exon boundaries were predicted using a combination of a BLAST search of the R. prolixus genome and Genie, an online software for splice site prediction []. Membrane topology of the receptors was predicted using the Transmembrane Prediction Tool plugin for Geneious. The potential phosphorylation sit […]


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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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