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 in publications

 (14)
PMCID: 5740500
PMID: 29242366
DOI: 10.15252/msb.20177728

[…] example, are included in transcripts by alternative promoter usage and by alternative cleavage and polyadenylation. mxes were predicted in the reconstructed genes using the algorithm implemented in webscipio (pillmann et al, ). the minimal exon length was set to 10 aa (–min_exon_length=10). webscipio determines the length of each exon (“search exon”) and generates a list of potential exonic […]

PMCID: 5583752
PMID: 28870165
DOI: 10.1186/s12862-017-1056-2

[…] domains []. this considerably increases the chance to observe intron position conservation even in genes from species with very low intron densities. myosin gene structures were reconstructed with webscipio []. the regions coding for the motor domains were than compared with genepainter [], which resolves conserved intron positions at nucleotide resolution. to obtain class-specific intron […]

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

[…] and sanger sequenced. obtained sequences were used to design further primers for ongoing sequence elongation. read assembly was performed with clc main workstation (rrid:scr_000354) 7.1., 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 […]

PMCID: 5243917
PMID: 27447459
DOI: 10.1007/s13353-016-0357-2

[…] 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 […]

PMCID: 4448529
PMID: 26024016
DOI: 10.1038/srep10652

[…] 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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