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Split-alignment of genomes finds orthologies more accurately.

Frith MC, Kawaguchi R - Genome Biol. (2015)

Bottom Line: Compared to previous animal genome alignments, it aligns thousands of locations differently and with much higher similarity, strongly suggesting that the previous alignments are non-orthologous.The previous methods suffer from an overly-strong assumption of long un-rearranged blocks.The new alignments should help find interesting and unusual features, such as fast-evolving elements and micro-rearrangements, which are confounded by alignment errors.

View Article: PubMed Central - PubMed

Affiliation: Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan. martin@cbrc.jp.

ABSTRACT
We present a new pair-wise genome alignment method, based on a simple concept of finding an optimal set of local alignments. It gains accuracy by not masking repeats, and by using a statistical model to quantify the (un)ambiguity of each alignment part. Compared to previous animal genome alignments, it aligns thousands of locations differently and with much higher similarity, strongly suggesting that the previous alignments are non-orthologous. The previous methods suffer from an overly-strong assumption of long un-rearranged blocks. The new alignments should help find interesting and unusual features, such as fast-evolving elements and micro-rearrangements, which are confounded by alignment errors.

No MeSH data available.


Related in: MedlinePlus

Genome alignments. Left: D. melanogaster (horizontal) versus D. pseudoobscura (vertical). Right: orangutan versus human chromosome 17. Red indicates same-strand alignments and blue indicates opposite-strand alignments
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Fig2: Genome alignments. Left: D. melanogaster (horizontal) versus D. pseudoobscura (vertical). Right: orangutan versus human chromosome 17. Red indicates same-strand alignments and blue indicates opposite-strand alignments

Mentions: The original meaning of “syntenic” is “on the same chromosome” [9]. Thus “conserved synteny” means conservation of being on the same chromosome. Comparison of Drosophila melanogaster and Drosophila pseudoobscura genomes shows striking synteny conservation: although these genomes are highly shuffled relative to each other, the shuffling is mostly within and not between chromosomes (Fig. 2).Fig. 2


Split-alignment of genomes finds orthologies more accurately.

Frith MC, Kawaguchi R - Genome Biol. (2015)

Genome alignments. Left: D. melanogaster (horizontal) versus D. pseudoobscura (vertical). Right: orangutan versus human chromosome 17. Red indicates same-strand alignments and blue indicates opposite-strand alignments
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4464727&req=5

Fig2: Genome alignments. Left: D. melanogaster (horizontal) versus D. pseudoobscura (vertical). Right: orangutan versus human chromosome 17. Red indicates same-strand alignments and blue indicates opposite-strand alignments
Mentions: The original meaning of “syntenic” is “on the same chromosome” [9]. Thus “conserved synteny” means conservation of being on the same chromosome. Comparison of Drosophila melanogaster and Drosophila pseudoobscura genomes shows striking synteny conservation: although these genomes are highly shuffled relative to each other, the shuffling is mostly within and not between chromosomes (Fig. 2).Fig. 2

Bottom Line: Compared to previous animal genome alignments, it aligns thousands of locations differently and with much higher similarity, strongly suggesting that the previous alignments are non-orthologous.The previous methods suffer from an overly-strong assumption of long un-rearranged blocks.The new alignments should help find interesting and unusual features, such as fast-evolving elements and micro-rearrangements, which are confounded by alignment errors.

View Article: PubMed Central - PubMed

Affiliation: Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan. martin@cbrc.jp.

ABSTRACT
We present a new pair-wise genome alignment method, based on a simple concept of finding an optimal set of local alignments. It gains accuracy by not masking repeats, and by using a statistical model to quantify the (un)ambiguity of each alignment part. Compared to previous animal genome alignments, it aligns thousands of locations differently and with much higher similarity, strongly suggesting that the previous alignments are non-orthologous. The previous methods suffer from an overly-strong assumption of long un-rearranged blocks. The new alignments should help find interesting and unusual features, such as fast-evolving elements and micro-rearrangements, which are confounded by alignment errors.

No MeSH data available.


Related in: MedlinePlus