Scaffolding low quality genomes using orthologous protein sequences | Zendy

Yang Li | Zendy; Richard R. Copley | Zendy

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Scaffolding low quality genomes using orthologous protein sequences

Author(s) -

Yang Li,

Richard R. Copley

Publication year - 2012

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bts661

Subject(s) - contig , genome , sequence assembly , biology , computational biology , ciona intestinalis , genetics , gene , gene expression , transcriptome

The ready availability of next-generation sequencing has led to a situation where it is easy to produce very fragmentary genome assemblies. We present a pipeline, SWiPS (Scaffolding With Protein Sequences), that uses orthologous proteins to improve low quality genome assemblies. The protein sequences are used as guides to scaffold existing contigs, while simultaneously allowing the gene structure to be predicted by homology.

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