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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
First step in completing a good bundle, maximizing the number of cycles. r is the number of incomplete paths in the bundle. Dots represent free ends before the step. kl is a cuttable edge in the input bundle, as are kgt and ghl in the new bundle. Output consists of two cycles (for r = 1) or one cycle and an open bundle with one fewer incomplete path (for r > 1).
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Figure 5: First step in completing a good bundle, maximizing the number of cycles. r is the number of incomplete paths in the bundle. Dots represent free ends before the step. kl is a cuttable edge in the input bundle, as are kgt and ghl in the new bundle. Output consists of two cycles (for r = 1) or one cycle and an open bundle with one fewer incomplete path (for r > 1).

Mentions: while there remain paths in the bundle as in Figure 5


Scaffold filling, contig fusion and comparative gene order inference.

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

First step in completing a good bundle, maximizing the number of cycles. r is the number of incomplete paths in the bundle. Dots represent free ends before the step. kl is a cuttable edge in the input bundle, as are kgt and ghl in the new bundle. Output consists of two cycles (for r = 1) or one cycle and an open bundle with one fewer incomplete path (for r > 1).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 5: First step in completing a good bundle, maximizing the number of cycles. r is the number of incomplete paths in the bundle. Dots represent free ends before the step. kl is a cuttable edge in the input bundle, as are kgt and ghl in the new bundle. Output consists of two cycles (for r = 1) or one cycle and an open bundle with one fewer incomplete path (for r > 1).
Mentions: while there remain paths in the bundle as in Figure 5

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