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  Predicting genes in closely related species with Scipio and WebScipio.

Kollmar, M. (2019). Predicting genes in closely related species with Scipio and WebScipio. In M. Kollmar (Ed.), Gene Prediction.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0003-7C4C-E Version Permalink: http://hdl.handle.net/21.11116/0000-0003-B549-F
Genre: Book Chapter

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3051167.pdf (Publisher version), 305KB
 
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 Creators:
Kollmar, M.1, Author              
Affiliations:
1Research Group of Systems Biology of Motor Proteins, MPI for biophysical chemistry, Max Planck Society, ou_578570              

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Free keywords: Eukaryotes; Gene prediction; Gene structure reconstruction; Sequenced genomes
 Abstract: Scipio and WebScipio are homology-based gene prediction software designed for annotating multigenic families and for transferring annotations from one species to closely related species. The strengths include the power to cope with sequencing-related problems such as sequencing errors and assemblies with short contigs but also the ability to correctly predict genes with unusually long introns and/or rather short exons. WebScipio is connected to diArk, the largest collection of eukaryotic genome assemblies, and thereby offers a very convenient way to correct existing annotations and to extend protein family datasets. WebScipio is also a key resource for researchers interested in mutually exclusive splicing, allowing to search for alternative exons not only in introns but also in up- and downstream regions in case of incompleteness of the search sequence. In this chapter, I describe how to use Scipio and WebScipio keeping a first-time user in mind.

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Language(s): eng - English
 Dates: 2019
 Publication Status: Published in print
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 Rev. Method: Peer
 Identifiers: DOI: 10.1007/978-1-4939-9173-0_11
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Title: Gene Prediction
Source Genre: Book
 Creator(s):
Kollmar, M.1, Editor            
Affiliations:
1 Research Group of Systems Biology of Motor Proteins, MPI for biophysical chemistry, Max Planck Society, ou_578570            
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Pages: - Volume / Issue: - Sequence Number: - Start / End Page: - Identifier: -

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Title: Methods in Molecular Biology
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Publ. Info: New York : Humana Press
Pages: - Volume / Issue: 1962 Sequence Number: - Start / End Page: 193 - 206 Identifier: ISBN: 978-1-4939-9172-3