Welcome to WebScipio

It is very time-consuming to always provide the latest genome assemblies. Thus, if you want Scipio/WebScipio to be continuously updated and its functionality extended in the future please properly cite the respective parts of the software!

Publications

Open Access Highly Accessed

If you use Scipio (command-line version), please cite:
O. Keller, F. Odronitz, M. Stanke, M. Kollmar & S. Waack (2008) Scipio: Using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species. BMC Bioinformatics 9, 278.

Open Access

If you use WebScipio, please cite:
K. Hatje, O. Keller, B. Hammesfahr, H. Pillmann S. Waack & M. Kollmar (2011) Cross-species protein sequence and gene structure prediction with fine-tuned Webscipio 2.0 and Scipio. BMC Research Notes 4, 265.

F. Odronitz, H. Pillmann, O. Keller, S. Waack & M. Kollmar (2008) WebScipio: An online tool for the determination of gene structures using protein sequences. BMC Genomics 9, 422.

Open Access Highly Accessed

If you use WebScipio's Search for Mutually Exclusive Exons, please cite:
H. Pillmann, K. Hatje, F. Odronitz, B. Hammesfahr & M. Kollmar (2011) Predicting mutually exclusive spliced exons based on exon length, splice site and reading frame conservation, and exon sequence homology. BMC Bioinformatics 12, 270.

Open Access

If you use WebScipio's Search for Tandem Gene Duplications, please cite:
K. Hatje & M. Kollmar (2011) Predicting Tandemly Arrayed Gene Duplicates with WebScipio. Gene Duplication, Felix Friedberg (Ed.), ISBN 978-953-307-387-3, InTech.

Newest Genomes

2014-09-16

Arachis_duranensis
Arachis duranensis v.1.0.0 (tsa_assembly2)
Taxonomy: Viridiplantae | Streptophyta | Streptophytina | . . . | Dalbergieae | Arachis
Contigs: 37379 | GC-Content: 0.431215311545148 | Bases: 34.7 | Filesize: 37.13MB
Arachis_ipaensis
Arachis ipaensis v.1.0.0 (tsa_assembly2)
Taxonomy: Viridiplantae | Streptophyta | Streptophytina | . . . | Dalbergieae | Arachis
Contigs: 29780 | GC-Content: 0.432647257978469 | Bases: 22.2 | Filesize: 23.98MB
Arachis_ipaensis
Arachis ipaensis v.1.0.0 (tsa_assembly3)
Taxonomy: Viridiplantae | Streptophyta | Streptophytina | . . . | Dalbergieae | Arachis
Contigs: 37379 | GC-Content: 0.431215311545148 | Bases: 34.7 | Filesize: 37.06MB
Arachis_ipaensis
Arachis ipaensis v.1.0.0 (tsa_assembly4)
Taxonomy: Viridiplantae | Streptophyta | Streptophytina | . . . | Dalbergieae | Arachis
Contigs: 30764 | GC-Content: 0.431043187218588 | Bases: 27.9 | Filesize: 29.7MB
Arachis_ipaensis
Arachis ipaensis v.1.0.0 (tsa_assembly5)
Taxonomy: Viridiplantae | Streptophyta | Streptophytina | . . . | Dalbergieae | Arachis
Contigs: 64014 | GC-Content: 0.431746256376172 | Bases: 53.0 | Filesize: 56.8MB

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WebScipio is a service by motorprotein.de

For many types of analyses, data about gene structure and locations of non-coding regions of genes are required. Although a vast amount of genomic sequence data is available, precise annotation of genes is lacking behind. Finding the corresponding gene of a given protein sequence by means of conventional tools is error prone, and cannot be completed without manual inspection which is time consuming and requires considerable experience.

Scipio is a tool based on the alignment program BLAT to determine the precise gene structure given a protein sequence and a genome. It identifies intron-exon borders and splice sites and is able to cope with sequencing errors and genes spanning several contigs in genomes that have not yet been assembled to supercontigs or chromosomes. Instead of producing a set of hits with varying confidence, Scipio gives the user a coherent summary of locations on the genome that code for the query protein. The output contains information about discrepancies that may result from sequencing errors. Scipio has also successfully been used to find homologous genes in closely related species.

Scipio work flow

Feedback

We would very much appreciate your feedback about any problems you may encounter. We also like to hear from you if WebScipio worked for you.

Restrictions and Licence

Using WebScipio and Scipio by non-academics requires permission. WebScipio and Scipio may be obtained upon request and used under a GNU General Public License.

link to kassiopeia
link to diark
link to cymobase
link to motorprotein.de
MPG
MPI for biophysical chemistry
Uni-Goettingen
Informatik Uni-Goettingen