Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (193K) Freely available
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 (23)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Panchenko, A. R.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Panchenko, A. R.
Related Collections
Right arrow Computational methods
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2003, Vol. 31, No. 2 683-689
© 2003 Oxford University Press

Finding weak similarities between proteins by sequence profile comparison

Anna R. Panchenko*

Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA

*Tel: +1 301 435 5891; Fax: +1 301 435 7794; Email: panch{at}ncbi.nlm.nih.gov

To improve the recognition of weak similarities between proteins a method of aligning two sequence profiles is proposed. It is shown that exploring the sequence space in the vicinity of the sequence with unknown properties significantly improves the performance of sequence alignment methods. Consistent with the previous observations the recognition sensitivity and alignment accuracy obtained by a profile–profile alignment method can be as much as 30% higher compared to the sequence–profile alignment method. It is demonstrated that the choice of score function and the diversity of the test profile are very important factors for achieving the maximum performance of the method, whereas the optimum range of these parameters depends on the level of similarity to be recognized.


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
 Nucleic Acids ResHome page
J. Soding, A. Biegert, and A. N. Lupas
The HHpred interactive server for protein homology detection and structure prediction
Nucleic Acids Res., July 1, 2005; 33(suppl_2): W244 - W248.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. Frenkel-Morgenstern, A. Singer, H. Bronfeld, and S. Pietrokovski
One-Block CYRCA: an automated procedure for identifying multiple-block alignments from single block queries
Nucleic Acids Res., July 1, 2005; 33(suppl_2): W281 - W283.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
M. Frenkel-Morgenstern, H. Voet, and S. Pietrokovski
Enhanced statistics for local alignment of multiple alignments improves prediction of protein function and structure
Bioinformatics, July 1, 2005; 21(13): 2950 - 2956.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
K. Ginalski, N. V. Grishin, A. Godzik, and L. Rychlewski
Practical lessons from protein structure prediction
Nucleic Acids Res., April 1, 2005; 33(6): 1874 - 1891.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
D. Gront and A. Kolinski
A new approach to prediction of short-range conformational propensities in proteins
Bioinformatics, April 1, 2005; 21(7): 981 - 987.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
J. Soding
Protein homology detection by HMM-HMM comparison
Bioinformatics, April 1, 2005; 21(7): 951 - 960.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
K. Ginalski, M. von Grotthuss, N. V. Grishin, and L. Rychlewski
Detecting distant homology with Meta-BASIC
Nucleic Acids Res., July 1, 2004; 32(suppl_2): W576 - W581.
[Abstract] [Full Text] [PDF]

Home page
 Protein Sci.Home page
G. Wang and R. L. Dunbrack Jr.
Scoring profile-to-profile sequence alignments
Protein Sci., June 1, 2004; 13(6): 1612 - 1626.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
N. C. W. Goonesekere and B. Lee
Frequency of gaps observed in a structurally aligned protein pair database suggests a simple gap penalty function
Nucleic Acids Res., May 20, 2004; 32(9): 2838 - 2843.
[Abstract] [Full Text] [PDF]

Home page
 Protein Sci.Home page
M. A. Marti-Renom, M.S. Madhusudhan, and A. Sali
Alignment of protein sequences by their profiles
Protein Sci., April 1, 2004; 13(4): 1071 - 1087.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
K. Ginalski, J. Pas, L. S. Wyrwicz, M. v. Grotthuss, J. M. Bujnicki, and L. Rychlewski
ORFeus: detection of distant homology using sequence profiles and predicted secondary structure
Nucleic Acids Res., July 1, 2003; 31(13): 3804 - 3807.
[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.