Improved Gene Structure Prediction with Scipio and WebScipio
Author Information
Author(s): Klas Hatje, Oliver Keller, Björn Hammesfahr, Holger Pillmann, Stephan Waack, Martin Kollmar
Primary Institution: Max-Planck-Institut für Biophysikalische Chemie
Hypothesis
The updated Scipio software can better reconstruct very short exons and intron splice sites for cross-species gene structure predictions.
Conclusion
The new version of Scipio can accurately reconstruct very short exons and predict almost all genes in cross-species searches, outperforming other software tested.
Supporting Evidence
- Scipio can correctly predict genes even if the ancestors of the species separated more than 100 million years ago.
- The new version of Scipio has been tested against several similar tools and has shown superior performance.
- WebScipio provides easy access to genome assemblies of about 640 eukaryotic species.
Takeaway
Scipio is a tool that helps scientists figure out the structure of genes in different species, even when the genes are very similar or have tiny parts missing.
Methodology
The software uses a pipeline that processes the output of the Blat program and implements the Needleman-Wunsch algorithm for better alignment of short sequences.
Limitations
The software may still struggle with very divergent sequences or when gene structures are highly fragmented across multiple contigs.
Digital Object Identifier (DOI)
Want to read the original?
Access the complete publication on the publisher's website