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Protocols

SpliceView specifications

Information


Unique identifier OMICS_09619
Name SpliceView
Interface Web user interface
Restrictions to use None
Input data Single sequence
Computer skills Basic
Stability No
Maintained No

Publication for SpliceView

SpliceView citations

 (35)
library_books

The role of transposable elements in functional evolution of amphioxus genome: the case of opsin gene family

2018
Sci Rep
PMCID: 5802833
PMID: 29410521
DOI: 10.1038/s41598-018-20683-9

[…] 3815.1/), from which most of the allelic scaffolds have been eliminated and is therefore a non-redundant mosaic of v1.0. All previously annotated opsin genes were validated through BLAST, Genscan and SpliceView analyses. In order to detect putative opsin homologs that were not previously reported, we conducted extensive keyword and BLAST searches. Newly identified opsin containing genomic loci wer […]

library_books

A deep intronic CLRN1 (USH3A) founder mutation generates an aberrant exon and underlies severe Usher syndrome on the Arabian Peninsula

2017
Sci Rep
PMCID: 5431179
PMID: 28469144
DOI: 10.1038/s41598-017-01577-8

[…] In silico analysis of the c.254–649T > G mutation using Spliceview and Maximum Entropy predicts that the mutation generates a novel donor splice site (score of 85 [Spliceview] and 8.76 [Maximum Entropy model]) compared to no predicted donor site in the wil […]

call_split

TIAM1 variants improve clinical outcome in neuroblastoma

2017
Oncotarget
PMCID: 5542186
PMID: 28423360
DOI: 10.18632/oncotarget.16787
call_split See protocol

[…] es. Investigation about the potential pathogenic role was done using databases (COSMIC, dbSNP, ClinVar (NCBI)), prediction algorithms (SIFT, PolyPhen-2 or Mutation Taster) or splice prediction tools (SpliceView, NetGene2, Human Splicing Finder, NNSplice). […]

call_split

Enniatin and Beauvericin Biosynthesis in Fusarium Species: Production Profiles and Structural Determinant Prediction

2017
Toxins
PMCID: 5331425
PMID: 28125067
DOI: 10.3390/toxins9020045
call_split See protocol

[…] Accession Number JF826561.1). The protein sequences were predicted using the Sequence Translation tools of the EMBOSS Programs (EMBL-EBI), manually curated with exon/intron boundary predictions from SpliceView (http://bioinfo4.itb.cnr.it/) and confirmed by RT-PCR of different partial sequences (Multifasta S1 and S2).The esyn1 mRNA from the F. verticillioides strain FGSC 7600 did not contain the 5 […]

call_split

A recurrent deletion in the SLC5A2 gene including the intron 7 branch site responsible for familial renal glucosuria

2016
Sci Rep
PMCID: 5036194
PMID: 27666404
DOI: 10.1038/srep33920
call_split See protocol

[…] ed. Four programs were used: BDGP (available at http://www.fruitfly.org), HSF 3.0 (available at http://www.umd.be/HSF3/HSF.html), NetGene2 (available at http://www.cbs.dtu.dk/services/NetGene2/), and Spliceview (available at http://bioinfo4.itb.cnr.it/~webgene/wwwspliceview_ex.html). […]

library_books

Computational Identification of Novel Genes: Current and Future Perspectives

2016
Bioinform Biol Insights
PMCID: 4970615
PMID: 27493475
DOI: 10.4137/BBI.S39950

[…] n one exon, the splice site prediction can be used to determine the exon boundaries of a gene and so the gene structure. An example of a splice site predictor based on multiple sequence alignments is SPLICEVIEW, whereas NetGene2 uses a neural network approach. Splice site prediction can be achieved using RNA-seq data with the KisSplice or FineSplice tools. The RSVP tool predicts splice variants of […]


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SpliceView institution(s)
Istituto di Tecnologie Biomediche Avanzate, Consiglio Nazionale Delle Ricerche, Milano, Italy

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