Limits...
A new repeat-masking method enables specific detection of homologous sequences.

Frith MC - Nucleic Acids Res. (2010)

Bottom Line: Homology search is confounded by simple repeats, which give rise to strong similarities that are not homologies.This method thoroughly eliminates spurious homology predictions for DNA-DNA, protein-protein and DNA-protein comparisons.Moreover, it enables accurate homology search for non-coding DNA with extreme A + T composition.

View Article: PubMed Central - PubMed

Affiliation: Computational Biology Research Center, Institute for Advanced Industrial Science and Technology, Sequence Analysis Team, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan. martin@cbrc.jp

ABSTRACT
Biological sequences are often analyzed by detecting homologous regions between them. Homology search is confounded by simple repeats, which give rise to strong similarities that are not homologies. Standard repeat-masking methods fail to eliminate this problem, and they are especially ill-suited to AT-rich DNA such as malaria and slime-mould genomes. We present a new repeat-masking method, TANTAN, which is motivated by the mechanisms that create simple repeats. This method thoroughly eliminates spurious homology predictions for DNA-DNA, protein-protein and DNA-protein comparisons. Moreover, it enables accurate homology search for non-coding DNA with extreme A + T composition.

Show MeSH

Related in: MedlinePlus

Alignments of reversed sequences after soft-masking repeats with tantan. Alignments between: (A) the A. thaliana genome and the reversed P. patens genome; (B) vertebrate proteins and reversed plant proteins. The dashed line is the observed number of alignments, and the solid line is the expected number for random sequences. (C) One of the alignments between A. thaliana (upper) and reversed P. patens (lower), with masked letters in lowercase.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3045581&req=5

Figure 8: Alignments of reversed sequences after soft-masking repeats with tantan. Alignments between: (A) the A. thaliana genome and the reversed P. patens genome; (B) vertebrate proteins and reversed plant proteins. The dashed line is the observed number of alignments, and the solid line is the expected number for random sequences. (C) One of the alignments between A. thaliana (upper) and reversed P. patens (lower), with masked letters in lowercase.

Mentions: We tested soft masking by comparing the A. thaliana genome to the reversed Physcomitrella patens genome, after masking both with tantan. We applied the masking during the seeding and gapless alignment phases of last, but not the gapped alignment phase. This soft masking failed to eliminate spurious similarities (Figure 8A), whereas hard masking succeeded (Figure 5B). Soft masking likewise failed for proteins (Figure 8B), and for DNA using trf instead of tantan (3).Figure 8.


A new repeat-masking method enables specific detection of homologous sequences.

Frith MC - Nucleic Acids Res. (2010)

Alignments of reversed sequences after soft-masking repeats with tantan. Alignments between: (A) the A. thaliana genome and the reversed P. patens genome; (B) vertebrate proteins and reversed plant proteins. The dashed line is the observed number of alignments, and the solid line is the expected number for random sequences. (C) One of the alignments between A. thaliana (upper) and reversed P. patens (lower), with masked letters in lowercase.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3045581&req=5

Figure 8: Alignments of reversed sequences after soft-masking repeats with tantan. Alignments between: (A) the A. thaliana genome and the reversed P. patens genome; (B) vertebrate proteins and reversed plant proteins. The dashed line is the observed number of alignments, and the solid line is the expected number for random sequences. (C) One of the alignments between A. thaliana (upper) and reversed P. patens (lower), with masked letters in lowercase.
Mentions: We tested soft masking by comparing the A. thaliana genome to the reversed Physcomitrella patens genome, after masking both with tantan. We applied the masking during the seeding and gapless alignment phases of last, but not the gapped alignment phase. This soft masking failed to eliminate spurious similarities (Figure 8A), whereas hard masking succeeded (Figure 5B). Soft masking likewise failed for proteins (Figure 8B), and for DNA using trf instead of tantan (3).Figure 8.

Bottom Line: Homology search is confounded by simple repeats, which give rise to strong similarities that are not homologies.This method thoroughly eliminates spurious homology predictions for DNA-DNA, protein-protein and DNA-protein comparisons.Moreover, it enables accurate homology search for non-coding DNA with extreme A + T composition.

View Article: PubMed Central - PubMed

Affiliation: Computational Biology Research Center, Institute for Advanced Industrial Science and Technology, Sequence Analysis Team, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan. martin@cbrc.jp

ABSTRACT
Biological sequences are often analyzed by detecting homologous regions between them. Homology search is confounded by simple repeats, which give rise to strong similarities that are not homologies. Standard repeat-masking methods fail to eliminate this problem, and they are especially ill-suited to AT-rich DNA such as malaria and slime-mould genomes. We present a new repeat-masking method, TANTAN, which is motivated by the mechanisms that create simple repeats. This method thoroughly eliminates spurious homology predictions for DNA-DNA, protein-protein and DNA-protein comparisons. Moreover, it enables accurate homology search for non-coding DNA with extreme A + T composition.

Show MeSH
Related in: MedlinePlus