The bulk and the tail of minimal absent words in genome sequences

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Aurell, Erik,1961-KTH,Beräkningsvetenskap och beräkningsteknik (CST),Aalto University, Finland,Computational Biological Physics, CBP (author)

The bulk and the tail of minimal absent words in genome sequences

Article/chapterEnglish2016

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2016-04-04
Institute of Physics (IOP),2016
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LIBRIS-ID:oai:DiVA.org:kth-173501
https://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-173501URI
https://doi.org/10.1088/1478-3975/13/2/026004DOI

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Language:English
Summary in:English

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QC 20161102
Minimal absent words (MAW) of a genomic sequence are subsequences that are absent themselves but the subwords of which are all present in the sequence. The characteristic distribution of genomic MAWs as a function of their length has been observed to be qualitatively similar for all living organisms, the bulk being rather short, and only relatively few being long. It has been an open issue whether the reason behind this phenomenon is statistical or reflects a biological mechanism, and what biological information is contained in absent words. % In this work we demonstrate that the bulk can be described by a probabilistic model of sampling words from random sequences, while the tail of long MAWs is of biological origin. We introduce the novel concept of a core of a minimal absent word, which are sequences present in the genome and closest to a given MAW. We show that in bacteria and yeast the cores of the longest MAWs, which exist in two or more copies, are located in highly conserved regions the most prominent example being ribosomal RNAs (rRNAs). We also show that while the distribution of the cores of long MAWs is roughly uniform over these genomes on a coarse-grained level, on a more detailed level it is strongly enhanced in 3' untranslated regions (UTRs) and, to a lesser extent, also in 5' UTRs. This indicates that MAWs and associated MAW cores correspond to fine-tuned evolutionary relationships, and suggest that they can be more widely used as markers for genomic complexity.

Subject headings and genre

NATURVETENSKAP Biologi Biofysik hsv//swe
NATURAL SCIENCES Biological Sciences Biophysics hsv//eng
NATURVETENSKAP Biologi Evolutionsbiologi hsv//swe
NATURAL SCIENCES Biological Sciences Evolutionary Biology hsv//eng
NATURVETENSKAP Biologi Genetik hsv//swe
NATURAL SCIENCES Biological Sciences Genetics hsv//eng
NATURVETENSKAP Data- och informationsvetenskap Bioinformatik hsv//swe
NATURAL SCIENCES Computer and Information Sciences Bioinformatics hsv//eng
NATURVETENSKAP Fysik hsv//swe
NATURAL SCIENCES Physical Sciences hsv//eng
Minimal absent word
copy-mutation evolution model
random sequence

Added entries (persons, corporate bodies, meetings, titles ...)

Innocenti, Nicolas,1986-KTH,Beräkningsvetenskap och beräkningsteknik (CST),The Hebrew University of Jerusalem, Israel,Computational Biological Physics, CBP(Swepub:kth)u1484r04 (author)
Zhou, Hai-JunState Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, China (author)
KTHBeräkningsvetenskap och beräkningsteknik (CST) (creator_code:org_t)

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In:Physical Biology: Institute of Physics (IOP)13:21478-39671478-3975

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NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Biophysics

NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Evolutionary Bio ...

NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Genetics

NATURAL SCIENCES: NATURAL SCIENCES; and Computer and Inf ...; and Bioinformatics

NATURAL SCIENCES: NATURAL SCIENCES; and Physical Science ...

Articles in the publication: Physical Biology

By the university: Royal Institute of Technology

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