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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

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.

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.

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.

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

2018-10-15

2018-04-20

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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.

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.

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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 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. 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. 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. 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 2018-10-15 Kluyveromyces marxianus LHW O v.1.0.0 (contigs) Taxonomy: Opisthokonta \| Fungi \| Dikarya \| . . . \| Saccharomycetaceae \| Kluyveromyces Contigs: 479 \| GC-Content: 0.40146501015507 \| Bases: 10.8 \| Filesize: 10.47MB Komagataella phaffii v.1.0.0 (contigs) Taxonomy: Opisthokonta \| Fungi \| Dikarya \| . . . \| Phaffomycetaceae \| Komagataella Contigs: 33 \| GC-Content: 0.41063923719793 \| Bases: 9.3 \| Filesize: 9.05MB Metschnikowia bicuspidata Baker2002 v.1.0.0 (contigs) Taxonomy: Opisthokonta \| Fungi \| Dikarya \| . . . \| Metschnikowiaceae \| Metschnikowia Contigs: 488 \| GC-Content: 0.511388768676602 \| Bases: 10.6 \| Filesize: 10.29MB Metschnikowia bicuspidata Baker2002 v.1.0.0 (supercontigs) Taxonomy: Opisthokonta \| Fungi \| Dikarya \| . . . \| Metschnikowiaceae \| Metschnikowia Contigs: 478 \| GC-Content: 0.511388768676602 \| Bases: 10.6 \| Filesize: 10.66MB 2018-04-20 Wickerhamiella galacta NRRL Y 17645 v.1.0.0 (contigs) Taxonomy: Opisthokonta \| Fungi \| Dikarya \| . . . \| Trichomonascaceae \| Wickerhamiella Contigs: 2137 \| GC-Content: 0.518062908185369 \| Bases: 9.6 \| Filesize: 9.58MB Show up to 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. 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.

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