Skip Navigation


Bioinformatics Advance Access originally published online on October 27, 2004
Bioinformatics 2005 21(7):902-911; doi:10.1093/bioinformatics/bti070
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow All Versions of this Article:
21/7/902    most recent
bti070v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (13)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Yu, Y.-K.
Right arrow Articles by Altschul, S. F.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Yu, Y.-K.
Right arrow Articles by Altschul, S. F.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Published by Oxford University Press 2004.

The construction of amino acid substitution matrices for the comparison of proteins with non-standard compositions

Yi-Kuo Yu and Stephen F. Altschul *

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda, MD 20894, USA

*To whom correspondence should be addressed.

Motivation: Amino acid substitution matrices play a central role in protein alignment methods. Standard log-odds matrices, such as those of the PAM and BLOSUM series, are constructed from large sets of protein alignments having implicit background amino acid frequencies. However, these matrices frequently are used to compare proteins with markedly different amino acid compositions, such as transmembrane proteins or proteins from organisms with strongly biased nucleotide compositions. It has been argued elsewhere that standard matrices are not ideal for such comparisons and, furthermore, a rationale has been presented for transforming a standard matrix for use in a non-standard compositional context.

Results: This paper presents the mathematical details underlying the compositional adjustment of amino acid or DNA substitution matrices.

Availability: Programs implementing the methods described are available from the authors upon request.

Contact: altschul{at}ncbi.nlm.nih.gov


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Mol Biol EvolHome page
K. L. Ring and A. R. O. Cavalcanti
Consequences of Stop Codon Reassignment on Protein Evolution in Ciliates with Alternative Genetic Codes
Mol. Biol. Evol., January 1, 2008; 25(1): 179 - 186.
[Abstract] [Full Text] [PDF]

Home page
 Eukaryot CellHome page
J. E. Coronado, S. Mneimneh, S. L. Epstein, W.-G. Qiu, and P. N. Lipke
Conserved Processes and Lineage-Specific Proteins in Fungal Cell Wall Evolution
Eukaryot. Cell, December 1, 2007; 6(12): 2269 - 2277.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Y.-K. Yu, E. M. Gertz, R. Agarwala, A. A. Schaffer, and S. F. Altschul
Retrieval accuracy, statistical significance and compositional similarity in protein sequence database searches
Nucleic Acids Res., November 6, 2006; 34(20): 5966 - 5973.
[Abstract] [Full Text] [PDF]

Home page
 Eukaryot CellHome page
J. E. Coronado, O. Attie, S. L. Epstein, W.-G. Qiu, and P. N. Lipke
Composition-Modified Matrices Improve Identification of Homologs of Saccharomyces cerevisiae Low-Complexity Glycoproteins.
Eukaryot. Cell, April 1, 2006; 5(4): 628 - 637.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.