Limits...
Scaffold filling, contig fusion and comparative gene order inference.

Muñoz A, Zheng C, Zhu Q, Albert VA, Rounsley S, Sankoff D - BMC Bioinformatics (2010)

Bottom Line: We model the relationship between the ratio of missing genes actually absent from the genome versus merely unsequenced ones, on one hand, and the increase of genomic distance after scaffold filling, on the other.We estimate the parameters of this model through simulations and by comparing the angiosperm genomes Ricinus communis and Vitis vinifera.The algorithm solves the comparison of genomes with 18,300 genes, including 4500 missing from one genome, in less than a minute on a MacBook, putting virtually all genomes within range of the method.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Mathematics and Statistics, University of Ottawa, Ottawa, K1N 6N5, Canada.

ABSTRACT

Background: There has been a trend in increasing the phylogenetic scope of genome sequencing without finishing the sequence of the genome. Increasing numbers of genomes are being published in scaffold or contig form. Rearrangement algorithms, however, including gene order-based phylogenetic tools, require whole genome data on gene order or syntenic block order. How then can we use rearrangement algorithms to compare genomes available in scaffold form only? Can the comparative evidence predict the location of unsequenced genes?

Results: Our method involves optimally filling in genes missing from the scaffolds, while incorporating the augmented scaffolds directly into the rearrangement algorithms as if they were chromosomes. This is accomplished by an exact, polynomial-time algorithm. We then correct for the number of extra fusion/fission operations required to make scaffolds comparable to full assemblies. We model the relationship between the ratio of missing genes actually absent from the genome versus merely unsequenced ones, on one hand, and the increase of genomic distance after scaffold filling, on the other. We estimate the parameters of this model through simulations and by comparing the angiosperm genomes Ricinus communis and Vitis vinifera.

Conclusions: The algorithm solves the comparison of genomes with 18,300 genes, including 4500 missing from one genome, in less than a minute on a MacBook, putting virtually all genomes within range of the method.

Show MeSH
Effect on D' of decreasing syntenic conservation for different proportions of non-gap-creating deletions.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2902449&req=5

Figure 7: Effect on D' of decreasing syntenic conservation for different proportions of non-gap-creating deletions.

Mentions: The simulations show that the value of D' increases with greater conserved synteny, and with higher proportions of non-gap-creating deletions. This is depicted in two ways in Figures 7 and 8. Of particular interest will be the case of D' = 0.37 indicated by the dashed line in both graphs. This case corresponds to the Ricinus-Vitis comparison as reported in the Results on Ricinus section below.


Scaffold filling, contig fusion and comparative gene order inference.

Muñoz A, Zheng C, Zhu Q, Albert VA, Rounsley S, Sankoff D - BMC Bioinformatics (2010)

Effect on D' of decreasing syntenic conservation for different proportions of non-gap-creating deletions.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2902449&req=5

Figure 7: Effect on D' of decreasing syntenic conservation for different proportions of non-gap-creating deletions.
Mentions: The simulations show that the value of D' increases with greater conserved synteny, and with higher proportions of non-gap-creating deletions. This is depicted in two ways in Figures 7 and 8. Of particular interest will be the case of D' = 0.37 indicated by the dashed line in both graphs. This case corresponds to the Ricinus-Vitis comparison as reported in the Results on Ricinus section below.

Bottom Line: We model the relationship between the ratio of missing genes actually absent from the genome versus merely unsequenced ones, on one hand, and the increase of genomic distance after scaffold filling, on the other.We estimate the parameters of this model through simulations and by comparing the angiosperm genomes Ricinus communis and Vitis vinifera.The algorithm solves the comparison of genomes with 18,300 genes, including 4500 missing from one genome, in less than a minute on a MacBook, putting virtually all genomes within range of the method.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Mathematics and Statistics, University of Ottawa, Ottawa, K1N 6N5, Canada.

ABSTRACT

Background: There has been a trend in increasing the phylogenetic scope of genome sequencing without finishing the sequence of the genome. Increasing numbers of genomes are being published in scaffold or contig form. Rearrangement algorithms, however, including gene order-based phylogenetic tools, require whole genome data on gene order or syntenic block order. How then can we use rearrangement algorithms to compare genomes available in scaffold form only? Can the comparative evidence predict the location of unsequenced genes?

Results: Our method involves optimally filling in genes missing from the scaffolds, while incorporating the augmented scaffolds directly into the rearrangement algorithms as if they were chromosomes. This is accomplished by an exact, polynomial-time algorithm. We then correct for the number of extra fusion/fission operations required to make scaffolds comparable to full assemblies. We model the relationship between the ratio of missing genes actually absent from the genome versus merely unsequenced ones, on one hand, and the increase of genomic distance after scaffold filling, on the other. We estimate the parameters of this model through simulations and by comparing the angiosperm genomes Ricinus communis and Vitis vinifera.

Conclusions: The algorithm solves the comparison of genomes with 18,300 genes, including 4500 missing from one genome, in less than a minute on a MacBook, putting virtually all genomes within range of the method.

Show MeSH