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PMID: 12801414 Published · ppublish English Comparative Study Journal Article

A method to assess compositional bias in biological sequences and its application to prion-like glutamine/asparagine-rich domains in eukaryotic proteomes.

Genome biology ·Vol. 4 ·No. 6 ·2003-00-00 ·Pages R40

Harrison PM, Gerstein M

Abstract

We have derived a novel method to assess compositional biases in biological sequences, which is based on finding the lowest-probability subsequences for a given residue-type set. As a case study, the distribution of prion-like glutamine/asparagine-rich ((Q+N)-rich) domains (which are linked to amyloidogenesis) was assessed for budding and fission yeasts and four other eukaryotes. We find more than 170 prion-like (Q+N)-rich regions in budding yeast, and, strikingly, many fewer in fission yeast. Also, some residues, such as tryptophan or isoleucine, are unlikely to form biased regions in any eukaryotic proteome.

MeSH Terms
Amino Acid Motifs/genetics Amino Acid Sequence/genetics Animals Asparagine/genetics Caenorhabditis elegans Proteins/chemistry,genetics Computational Biology/methods,statistics & numerical data Drosophila Proteins/chemistry,genetics Eukaryotic Cells/chemistry,metabolism Fungal Proteins/chemistry,genetics Glutamine/genetics Humans Molecular Sequence Data Prions/chemistry,genetics Protein Structure, Tertiary/genetics Proteome/genetics Saccharomycetales/genetics Schizosaccharomyces/genetics Schizosaccharomyces pombe Proteins/chemistry,genetics Selection, Genetic Sequence Analysis, Protein/methods,statistics & numerical data
Chemicals
Caenorhabditis elegans Proteins Drosophila Proteins Fungal Proteins Prions Proteome Schizosaccharomyces pombe Proteins Glutamine Asparagine
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Harrison Paul M
Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520-8114, USA. harrison@csb.yale.edu
Gerstein Mark
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Article Info
Journal
Genome biology
Abbr.
Genome Biol
ISSN
1474-760X
DOI
10.1186/gb-2003-4-6-r40
Email
harrison@csb.yale.edu
Published
2003-00-00
Epub
2003-00-30
Pages
R40
Language
English
Region
England
NLM ID
100960660
PMCID
PMC193619
Subset
IM
External Links
PubMed source DOI: 10.1186/gb-2003-4-6-r40 PMC Full Text View journal details
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