Limits...
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

Comparison of LAST (1-split, pre-masked) and UCSC genome alignments. The panel headings show query-reference. For each “different” LAST alignment (no pair of aligned bases in common with UCSC) whose human segment is covered by one UCSC alignment, that segment’s alignment scores are compared
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig3: Comparison of LAST (1-split, pre-masked) and UCSC genome alignments. The panel headings show query-reference. For each “different” LAST alignment (no pair of aligned bases in common with UCSC) whose human segment is covered by one UCSC alignment, that segment’s alignment scores are compared

Mentions: The new method was used to align the human and chimp genomes, with standard repeat-masking at first. To facilitate comparison with the UCSC alignments, the same scoring scheme was used (human-chimp.v2, Table 1). This produced 371977 1-split alignments (with human as query), of which 15084 are “different” from UCSC, meaning no pair of aligned bases in common. For 6845 of these different alignments, the alignment’s human segment is 100 % covered by (i.e. contained in) one UCSC alignment: so we can compare the alignment scores for this (exact same) human segment. LAST’s score is higher in 95 % of cases (Fig. 3). For human versus dog, LAST’s score is higher in 90 % of cases.Fig. 3


Split-alignment of genomes finds orthologies more accurately.

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

Comparison of LAST (1-split, pre-masked) and UCSC genome alignments. The panel headings show query-reference. For each “different” LAST alignment (no pair of aligned bases in common with UCSC) whose human segment is covered by one UCSC alignment, that segment’s alignment scores are compared
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig3: Comparison of LAST (1-split, pre-masked) and UCSC genome alignments. The panel headings show query-reference. For each “different” LAST alignment (no pair of aligned bases in common with UCSC) whose human segment is covered by one UCSC alignment, that segment’s alignment scores are compared
Mentions: The new method was used to align the human and chimp genomes, with standard repeat-masking at first. To facilitate comparison with the UCSC alignments, the same scoring scheme was used (human-chimp.v2, Table 1). This produced 371977 1-split alignments (with human as query), of which 15084 are “different” from UCSC, meaning no pair of aligned bases in common. For 6845 of these different alignments, the alignment’s human segment is 100 % covered by (i.e. contained in) one UCSC alignment: so we can compare the alignment scores for this (exact same) human segment. LAST’s score is higher in 95 % of cases (Fig. 3). For human versus dog, LAST’s score is higher in 90 % of cases.Fig. 3

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