Bias of purine stretches in sequenced chromosomes

David Ussery, Dikeos Mario Soumpasis, Søren Brunak, Hans Henrik Stærfeldt, Peder Worning, Anders Stærmose Krogh

    Research output: Contribution to journalJournal articleResearchpeer-review

    Abstract

    We examined more than 700 DNA sequences (full length chromosomes and plasmids) for stretches of purines (R) or pyrimidines (Y) and alternating YR stretches; such regions will likely adopt structures which are different from the canonical B-form. Since one turn of the DNA helix is roughly 10 bp, we measured the fraction of each genome which contains purine (or pyrimidine) tracts of lengths of 10 by or longer (hereafter referred to as 'purine tracts'), as well as stretches of alternating pyrimidines/purine ('pyr/pur tracts') of the same length. Using this criteria, a random sequence would be expected to contain 1.0% of purine tracts and also 1.0% of the alternating pyr/pur tracts. In the vast majority of cases, there are more purine tracts than would be expected from a random sequence, with an average of 3.5%, significantly larger than the expectation value. The fraction of the chromosomes containing pyr/pur tracts was slightly less than expected, with an average of 0.8%. One of the most surprising findings is a clear difference in the length distributions of the regions studied between prokaryotes and eukaryotes. Whereas short-range correlations can explain the length distributions in prokaryotes, in eukaryotes there is an abundance of long stretches of purines or alternating purine/pyrimidine tracts, which cannot be explained in this way; these sequences are likely to play an important role in eukaryotic chromosome organisation.
    Original languageEnglish
    JournalComputers & Chemistry
    Volume26
    Issue number5
    Pages (from-to)531-541
    ISSN0097-8485
    Publication statusPublished - 2002

    Cite this

    Ussery, D., Soumpasis, D. M., Brunak, S., Stærfeldt, H. H., Worning, P., & Krogh, A. S. (2002). Bias of purine stretches in sequenced chromosomes. Computers & Chemistry, 26(5), 531-541.
    Ussery, David ; Soumpasis, Dikeos Mario ; Brunak, Søren ; Stærfeldt, Hans Henrik ; Worning, Peder ; Krogh, Anders Stærmose. / Bias of purine stretches in sequenced chromosomes. In: Computers & Chemistry. 2002 ; Vol. 26, No. 5. pp. 531-541.
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    abstract = "We examined more than 700 DNA sequences (full length chromosomes and plasmids) for stretches of purines (R) or pyrimidines (Y) and alternating YR stretches; such regions will likely adopt structures which are different from the canonical B-form. Since one turn of the DNA helix is roughly 10 bp, we measured the fraction of each genome which contains purine (or pyrimidine) tracts of lengths of 10 by or longer (hereafter referred to as 'purine tracts'), as well as stretches of alternating pyrimidines/purine ('pyr/pur tracts') of the same length. Using this criteria, a random sequence would be expected to contain 1.0{\%} of purine tracts and also 1.0{\%} of the alternating pyr/pur tracts. In the vast majority of cases, there are more purine tracts than would be expected from a random sequence, with an average of 3.5{\%}, significantly larger than the expectation value. The fraction of the chromosomes containing pyr/pur tracts was slightly less than expected, with an average of 0.8{\%}. One of the most surprising findings is a clear difference in the length distributions of the regions studied between prokaryotes and eukaryotes. Whereas short-range correlations can explain the length distributions in prokaryotes, in eukaryotes there is an abundance of long stretches of purines or alternating purine/pyrimidine tracts, which cannot be explained in this way; these sequences are likely to play an important role in eukaryotic chromosome organisation.",
    author = "David Ussery and Soumpasis, {Dikeos Mario} and S{\o}ren Brunak and St{\ae}rfeldt, {Hans Henrik} and Peder Worning and Krogh, {Anders St{\ae}rmose}",
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    Ussery, D, Soumpasis, DM, Brunak, S, Stærfeldt, HH, Worning, P & Krogh, AS 2002, 'Bias of purine stretches in sequenced chromosomes', Computers & Chemistry, vol. 26, no. 5, pp. 531-541.

    Bias of purine stretches in sequenced chromosomes. / Ussery, David; Soumpasis, Dikeos Mario; Brunak, Søren; Stærfeldt, Hans Henrik; Worning, Peder; Krogh, Anders Stærmose.

    In: Computers & Chemistry, Vol. 26, No. 5, 2002, p. 531-541.

    Research output: Contribution to journalJournal articleResearchpeer-review

    TY - JOUR

    T1 - Bias of purine stretches in sequenced chromosomes

    AU - Ussery, David

    AU - Soumpasis, Dikeos Mario

    AU - Brunak, Søren

    AU - Stærfeldt, Hans Henrik

    AU - Worning, Peder

    AU - Krogh, Anders Stærmose

    PY - 2002

    Y1 - 2002

    N2 - We examined more than 700 DNA sequences (full length chromosomes and plasmids) for stretches of purines (R) or pyrimidines (Y) and alternating YR stretches; such regions will likely adopt structures which are different from the canonical B-form. Since one turn of the DNA helix is roughly 10 bp, we measured the fraction of each genome which contains purine (or pyrimidine) tracts of lengths of 10 by or longer (hereafter referred to as 'purine tracts'), as well as stretches of alternating pyrimidines/purine ('pyr/pur tracts') of the same length. Using this criteria, a random sequence would be expected to contain 1.0% of purine tracts and also 1.0% of the alternating pyr/pur tracts. In the vast majority of cases, there are more purine tracts than would be expected from a random sequence, with an average of 3.5%, significantly larger than the expectation value. The fraction of the chromosomes containing pyr/pur tracts was slightly less than expected, with an average of 0.8%. One of the most surprising findings is a clear difference in the length distributions of the regions studied between prokaryotes and eukaryotes. Whereas short-range correlations can explain the length distributions in prokaryotes, in eukaryotes there is an abundance of long stretches of purines or alternating purine/pyrimidine tracts, which cannot be explained in this way; these sequences are likely to play an important role in eukaryotic chromosome organisation.

    AB - We examined more than 700 DNA sequences (full length chromosomes and plasmids) for stretches of purines (R) or pyrimidines (Y) and alternating YR stretches; such regions will likely adopt structures which are different from the canonical B-form. Since one turn of the DNA helix is roughly 10 bp, we measured the fraction of each genome which contains purine (or pyrimidine) tracts of lengths of 10 by or longer (hereafter referred to as 'purine tracts'), as well as stretches of alternating pyrimidines/purine ('pyr/pur tracts') of the same length. Using this criteria, a random sequence would be expected to contain 1.0% of purine tracts and also 1.0% of the alternating pyr/pur tracts. In the vast majority of cases, there are more purine tracts than would be expected from a random sequence, with an average of 3.5%, significantly larger than the expectation value. The fraction of the chromosomes containing pyr/pur tracts was slightly less than expected, with an average of 0.8%. One of the most surprising findings is a clear difference in the length distributions of the regions studied between prokaryotes and eukaryotes. Whereas short-range correlations can explain the length distributions in prokaryotes, in eukaryotes there is an abundance of long stretches of purines or alternating purine/pyrimidine tracts, which cannot be explained in this way; these sequences are likely to play an important role in eukaryotic chromosome organisation.

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    JO - Computers and Chemistry

    JF - Computers and Chemistry

    SN - 0097-8485

    IS - 5

    ER -

    Ussery D, Soumpasis DM, Brunak S, Stærfeldt HH, Worning P, Krogh AS. Bias of purine stretches in sequenced chromosomes. Computers & Chemistry. 2002;26(5):531-541.