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WebScipio specifications

Information


Unique identifier OMICS_06096
Name WebScipio
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability No
Maintained Yes

Publications for WebScipio

WebScipio citations

 (18)
library_books

The landscape of human mutually exclusive splicing

2017
Mol Syst Biol
PMCID: 5740500
PMID: 29242366
DOI: 10.15252/msb.20177728

[…] B entries, the full‐length proteins were fetched from UniProt KB (UniProt Consortium, ) or GenBank (Benson et al, ) and the corresponding gene structures of the eukaryotic proteins reconstructed with WebScipio (Hatje et al, ). In Allora, all PDBs belonging to the same UniProt or GenBank entries are connected. BLAST+ (Camacho et al, ) was used to search for the most similar UniProt/GenBank protein […]

library_books

Myosin repertoire expansion coincides with eukaryotic diversification in the Mesoproterozoic era

2017
BMC Evol Biol
PMCID: 5583752
PMID: 28870165
DOI: 10.1186/s12862-017-1056-2

[…] wed two strategies to identify and assemble further myosin sequences. A) We reconstructed homologs in species belonging to taxa for which complete myosin repertoires have already been determined with WebScipio [] using the myosins of the closest related species as query sequences and adjusting the search parameters to allow the correct or almost correct reconstruction of protein homologs down to a […]

library_books

Co expression of xenopsin and rhabdomeric opsin in photoreceptors bearing microvilli and cilia

2017
eLife
PMCID: 5648526
PMID: 28876222
DOI: 10.7554/eLife.23435.121

[…] WebScipio () was used to determine the gene structure including the respective intron phases of all those opsin sequences included in our phylogenetic analysis for which genomic data were available (1 […]

library_books

Fine Tuning Motile Cilia and Flagella: Evolution of the Dynein Motor Proteins from Plants to Humans at High Resolution

2016
Mol Biol Evol
PMCID: 5100056
PMID: 27880711
DOI: 10.1093/molbev/msw213

[…] , EST and TSA data have been analyzed to help in the annotation process. Protein sequences from closely related species have been obtained using the cross-species gene reconstruction functionality of WebScipio () using the dyneins of the closest related species as query sequences and adjusting the search parameters to allow the correct or almost correct reconstruction of protein homologs down to a […]

library_books

Genome wide identification, characterisation and expression profiles of calcium dependent protein kinase genes in barley (Hordeum vulgare L.)

2016
J Appl Genet
PMCID: 5243917
PMID: 27447459
DOI: 10.1007/s13353-016-0357-2

[…] e Ensembl Plant genomes against the Pfam v13 database (Punta et al. ) with HMMER 3.0 software (Finn et al. ). The precise exon/intron structures of CDPK genes were determined using Scipio (http://www.webscipio.org/) based on the corresponding protein sequences (Keller et al. ). The presence of myristoylation motifs at the N-terminal domain were predicted using the Eukaryotic Linear Motif resource […]

library_books

Polyphyly of nuclear lamin genes indicates an early eukaryotic origin of the metazoan type intermediate filament proteins

2015
Sci Rep
PMCID: 4448529
PMID: 26024016
DOI: 10.1038/srep10652

[…] otif, are supported by many EST clones. Gene prediction is highly facilitated if homologs of closely related species have already been obtained. In such cases, I used the gene reconstruction software WebScipio with default cross-species search parameters. By this approach, better gene predictions are obtained and even gene duplicates correctly determined. However, this requires a certain sequence […]

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WebScipio institution(s)
Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany

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