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Motif-aware PRALINE:improving the alignment of motif regions

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Τίτλος: Motif-aware PRALINE:improving the alignment of motif regions
Συγγραφείς: Dijkstra, Maurits, Bawono, Punto, Abeln, Sanne, Feenstra, K. Anton, Fokkink, Wan, Heringa, Jaap
Πηγή: Dijkstra, M, Bawono, P, Abeln, S, Feenstra, K A, Fokkink, W & Heringa, J 2018, 'Motif-aware PRALINE : improving the alignment of motif regions', PLoS Computational Biology, vol. 14, no. 11, e1006547. https://doi.org/10.1371/journal.pcbi.1006547
Έτος έκδοσης: 2018
Θεματικοί όροι: Algorithms, Amino Acid Motifs, Amino Acid Sequence, Conserved Sequence, DNA/chemistry, HIV-1/chemistry, Proteins/chemistry, Sequence Alignment/standards, Sequence Homology, Amino Acid, env Gene Products, Human Immunodeficiency Virus/chemistry, /dk/atira/pure/sustainabledevelopmentgoals/good_health_and_well_being, name=SDG 3 - Good Health and Well-being
Περιγραφή: Protein or DNA motifs are sequence regions which possess biological importance. These regions are often highly conserved among homologous sequences. The generation of multiple sequence alignments (MSAs) with a correct alignment of the conserved sequence motifs is still difficult to achieve, due to the fact that the contribution of these typically short fragments is overshadowed by the rest of the sequence. Here we extended the PRALINE multiple sequence alignment program with a novel motif-aware MSA algorithm in order to address this shortcoming. This method can incorporate explicit information about the presence of externally provided sequence motifs, which is then used in the dynamic programming step by boosting the amino acid substitution matrix towards the motif. The strength of the boost is controlled by a parameter, α. Using a benchmark set of alignments we confirm that a good compromise can be found that improves the matching of motif regions while not significantly reducing the overall alignment quality. By estimating α on an unrelated set of reference alignments we find there is indeed a strong conservation signal for motifs. A number of typical but difficult MSA use cases are explored to exemplify the problems in correctly aligning functional sequence motifs and how the motif-aware alignment method can be employed to alleviate these problems.
Τύπος εγγράφου: article in journal/newspaper
Περιγραφή αρχείου: application/pdf
Γλώσσα: English
ISSN: 1553-734X
1553-7358
Relation: info:eu-repo/semantics/altIdentifier/pmid/30383764; info:eu-repo/semantics/altIdentifier/pissn/1553-734X; info:eu-repo/semantics/altIdentifier/eissn/1553-7358
DOI: 10.1371/journal.pcbi.1006547
Διαθεσιμότητα: https://research.tue.nl/en/publications/dbd99d99-f042-4a82-ac26-a52b1bba1077
https://doi.org/10.1371/journal.pcbi.1006547
https://pure.tue.nl/ws/files/115933536/journal.pcbi.1006547_2_.pdf
https://www.scopus.com/pages/publications/85056514138
Rights: info:eu-repo/semantics/openAccess
Αριθμός Καταχώρησης: edsbas.3186B6B2
Βάση Δεδομένων: BASE
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  – Url: https://research.tue.nl/en/publications/dbd99d99-f042-4a82-ac26-a52b1bba1077#
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  Data: Motif-aware PRALINE:improving the alignment of motif regions
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  Data: <searchLink fieldCode="AR" term="%22Dijkstra%2C+Maurits%22">Dijkstra, Maurits</searchLink><br /><searchLink fieldCode="AR" term="%22Bawono%2C+Punto%22">Bawono, Punto</searchLink><br /><searchLink fieldCode="AR" term="%22Abeln%2C+Sanne%22">Abeln, Sanne</searchLink><br /><searchLink fieldCode="AR" term="%22Feenstra%2C+K%2E+Anton%22">Feenstra, K. Anton</searchLink><br /><searchLink fieldCode="AR" term="%22Fokkink%2C+Wan%22">Fokkink, Wan</searchLink><br /><searchLink fieldCode="AR" term="%22Heringa%2C+Jaap%22">Heringa, Jaap</searchLink>
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  Data: Dijkstra, M, Bawono, P, Abeln, S, Feenstra, K A, Fokkink, W & Heringa, J 2018, 'Motif-aware PRALINE : improving the alignment of motif regions', PLoS Computational Biology, vol. 14, no. 11, e1006547. https://doi.org/10.1371/journal.pcbi.1006547
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  Data: 2018
– Name: Subject
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  Data: <searchLink fieldCode="DE" term="%22Algorithms%22">Algorithms</searchLink><br /><searchLink fieldCode="DE" term="%22Amino+Acid+Motifs%22">Amino Acid Motifs</searchLink><br /><searchLink fieldCode="DE" term="%22Amino+Acid+Sequence%22">Amino Acid Sequence</searchLink><br /><searchLink fieldCode="DE" term="%22Conserved+Sequence%22">Conserved Sequence</searchLink><br /><searchLink fieldCode="DE" term="%22DNA%2Fchemistry%22">DNA/chemistry</searchLink><br /><searchLink fieldCode="DE" term="%22HIV-1%2Fchemistry%22">HIV-1/chemistry</searchLink><br /><searchLink fieldCode="DE" term="%22Proteins%2Fchemistry%22">Proteins/chemistry</searchLink><br /><searchLink fieldCode="DE" term="%22Sequence+Alignment%2Fstandards%22">Sequence Alignment/standards</searchLink><br /><searchLink fieldCode="DE" term="%22Sequence+Homology%22">Sequence Homology</searchLink><br /><searchLink fieldCode="DE" term="%22Amino+Acid%22">Amino Acid</searchLink><br /><searchLink fieldCode="DE" term="%22env+Gene+Products%22">env Gene Products</searchLink><br /><searchLink fieldCode="DE" term="%22Human+Immunodeficiency+Virus%2Fchemistry%22">Human Immunodeficiency Virus/chemistry</searchLink><br /><searchLink fieldCode="DE" term="%22%2Fdk%2Fatira%2Fpure%2Fsustainabledevelopmentgoals%2Fgood%5Fhealth%5Fand%5Fwell%5Fbeing%22">/dk/atira/pure/sustainabledevelopmentgoals/good_health_and_well_being</searchLink><br /><searchLink fieldCode="DE" term="%22name=SDG+3+-+Good+Health+and+Well-being%22">name=SDG 3 - Good Health and Well-being</searchLink>
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  Label: Description
  Group: Ab
  Data: Protein or DNA motifs are sequence regions which possess biological importance. These regions are often highly conserved among homologous sequences. The generation of multiple sequence alignments (MSAs) with a correct alignment of the conserved sequence motifs is still difficult to achieve, due to the fact that the contribution of these typically short fragments is overshadowed by the rest of the sequence. Here we extended the PRALINE multiple sequence alignment program with a novel motif-aware MSA algorithm in order to address this shortcoming. This method can incorporate explicit information about the presence of externally provided sequence motifs, which is then used in the dynamic programming step by boosting the amino acid substitution matrix towards the motif. The strength of the boost is controlled by a parameter, α. Using a benchmark set of alignments we confirm that a good compromise can be found that improves the matching of motif regions while not significantly reducing the overall alignment quality. By estimating α on an unrelated set of reference alignments we find there is indeed a strong conservation signal for motifs. A number of typical but difficult MSA use cases are explored to exemplify the problems in correctly aligning functional sequence motifs and how the motif-aware alignment method can be employed to alleviate these problems.
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  Data: 10.1371/journal.pcbi.1006547
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  Data: https://research.tue.nl/en/publications/dbd99d99-f042-4a82-ac26-a52b1bba1077<br />https://doi.org/10.1371/journal.pcbi.1006547<br />https://pure.tue.nl/ws/files/115933536/journal.pcbi.1006547_2_.pdf<br />https://www.scopus.com/pages/publications/85056514138
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        Value: 10.1371/journal.pcbi.1006547
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      – Text: English
    Subjects:
      – SubjectFull: Algorithms
        Type: general
      – SubjectFull: Amino Acid Motifs
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      – SubjectFull: Amino Acid Sequence
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