A profile-based protein sequence alignment algorithm for a domain clustering database

Lin Xu; Fa Zhang; Zhiyong Liu

doi:10.1109/CIBCB.2006.330990

A profile-based protein sequence alignment algorithm for a domain clustering database

Lin Xu^*, Fa Zhang, Zhiyong Liu

^*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

Abstract

Aiming at the two main shortcomings in Homology Modeling, we have designed and established a domain clustering database. Searching the database is a fundamental work for it. However, current alignment algorithms are mainly based on the sequences, ignoring the structure conservation in domain. This paper proposed a profile-based alignment which considers the structure information into the profile, based on the character of our domain database. We designed an experiment within the database. The results show that both the quality and sensitivity of our scheme are better than pure Smith-Waterman and sequence-based profile algorithms. We strongly believe that this work can help to improve the protein structure prediction.

Original language	English
Title of host publication	Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'06
Pages	193-200
Number of pages	8
DOIs	https://doi.org/10.1109/CIBCB.2006.330990
Publication status	Published - 2006
Externally published	Yes
Event	3rd Computational Intelligence in Bioinformatics and Computational Biology Symposium, CIBCB - Toronto, ON, Canada Duration: 28 Sept 2006 → 29 Sept 2006

Publication series

Name	Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'06

Conference

Conference	3rd Computational Intelligence in Bioinformatics and Computational Biology Symposium, CIBCB
Country/Territory	Canada
City	Toronto, ON
Period	28/09/06 → 29/09/06

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10.1109/CIBCB.2006.330990

Cite this

Xu, L., Zhang, F., & Liu, Z. (2006). A profile-based protein sequence alignment algorithm for a domain clustering database. In Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'06 (pp. 193-200). Article 4133172 (Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'06). https://doi.org/10.1109/CIBCB.2006.330990

Xu, Lin ; Zhang, Fa ; Liu, Zhiyong. / A profile-based protein sequence alignment algorithm for a domain clustering database. Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'06. 2006. pp. 193-200 (Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'06).

@inproceedings{028f3b4f12f347d6982f2673e497adb4,

title = "A profile-based protein sequence alignment algorithm for a domain clustering database",

abstract = "Aiming at the two main shortcomings in Homology Modeling, we have designed and established a domain clustering database. Searching the database is a fundamental work for it. However, current alignment algorithms are mainly based on the sequences, ignoring the structure conservation in domain. This paper proposed a profile-based alignment which considers the structure information into the profile, based on the character of our domain database. We designed an experiment within the database. The results show that both the quality and sensitivity of our scheme are better than pure Smith-Waterman and sequence-based profile algorithms. We strongly believe that this work can help to improve the protein structure prediction.",

author = "Lin Xu and Fa Zhang and Zhiyong Liu",

year = "2006",

doi = "10.1109/CIBCB.2006.330990",

language = "English",

isbn = "1424406234",

series = "Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'06",

pages = "193--200",

booktitle = "Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'06",

note = "3rd Computational Intelligence in Bioinformatics and Computational Biology Symposium, CIBCB ; Conference date: 28-09-2006 Through 29-09-2006",

}

Xu, L, Zhang, F & Liu, Z 2006, A profile-based protein sequence alignment algorithm for a domain clustering database. in Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'06., 4133172, Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'06, pp. 193-200, 3rd Computational Intelligence in Bioinformatics and Computational Biology Symposium, CIBCB, Toronto, ON, Canada, 28/09/06. https://doi.org/10.1109/CIBCB.2006.330990

A profile-based protein sequence alignment algorithm for a domain clustering database. / Xu, Lin; Zhang, Fa; Liu, Zhiyong.
Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'06. 2006. p. 193-200 4133172 (Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'06).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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N2 - Aiming at the two main shortcomings in Homology Modeling, we have designed and established a domain clustering database. Searching the database is a fundamental work for it. However, current alignment algorithms are mainly based on the sequences, ignoring the structure conservation in domain. This paper proposed a profile-based alignment which considers the structure information into the profile, based on the character of our domain database. We designed an experiment within the database. The results show that both the quality and sensitivity of our scheme are better than pure Smith-Waterman and sequence-based profile algorithms. We strongly believe that this work can help to improve the protein structure prediction.

AB - Aiming at the two main shortcomings in Homology Modeling, we have designed and established a domain clustering database. Searching the database is a fundamental work for it. However, current alignment algorithms are mainly based on the sequences, ignoring the structure conservation in domain. This paper proposed a profile-based alignment which considers the structure information into the profile, based on the character of our domain database. We designed an experiment within the database. The results show that both the quality and sensitivity of our scheme are better than pure Smith-Waterman and sequence-based profile algorithms. We strongly believe that this work can help to improve the protein structure prediction.

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SN - 9781424406234

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Xu L, Zhang F, Liu Z. A profile-based protein sequence alignment algorithm for a domain clustering database. In Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'06. 2006. p. 193-200. 4133172. (Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'06). doi: 10.1109/CIBCB.2006.330990

A profile-based protein sequence alignment algorithm for a domain clustering database

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