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Updated: May 16, 2026
09:37
An Integrated Approach for Microprotein Identification and Sequence Analysis
Published on: July 12, 2022
Scaffolding low quality genomes using orthologous protein sequences
1Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK. yang.li@well.ox.ac.uk
Bioinformatics (Oxford, England)
|November 20, 2012
Summary
SWiPS (Scaffolding With Protein Sequences) improves fragmented genome assemblies using orthologous proteins. This method enhances gene space representation and scaffold accuracy, even with low-quality data.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Next-generation sequencing generates highly fragmented genome assemblies.
- Low-quality assemblies pose challenges for downstream genomic analyses.
- Existing assembly methods struggle with large intergenic regions in eukaryotes.
Purpose of the Study:
- To present SWiPS (Scaffolding With Protein Sequences), a novel pipeline for improving fragmented genome assemblies.
- To utilize orthologous protein sequences as guides for scaffolding and gene prediction.
- To enhance the quality and completeness of low-quality genome assemblies.
Main Methods:
- SWiPS employs orthologous protein sequences to scaffold existing contigs.
- The pipeline simultaneously predicts gene structures through homology.
- It does not require high N50 values or complete proteins on single contigs.
Main Results:
- SWiPS improved N50 by ~20% for *Ciona intestinalis* and *Homo sapiens* assemblies.
- Gene space representation increased by >110% for *Callorhinchus milii* and 20-40% for *C. intestinalis*.
- Scaffold error rates were low, with 85-90% of scaffolds fully correct and >95% of local contig joins accurate.
Conclusions:
- SWiPS effectively improves fragmented genome assemblies using protein sequence information.
- The method enhances gene space recovery and scaffold accuracy in diverse eukaryotic genomes.
- SWiPS offers a valuable tool for researchers working with low-quality or fragmentary genome assemblies.
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