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Activity Number:
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325
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Type:
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Topic Contributed
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Date/Time:
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Tuesday, July 31, 2007 : 2:00 PM to 3:50 PM
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Sponsor:
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IMS
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| Abstract - #308463 |
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Title:
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Protein Multiple Alignment Using Primary and Secondary Structure Information
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Author(s):
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Nak-Kyeong Kim*+ and Jun Xie
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Companies:
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National Institutes of Health and Purdue University
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Address:
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NCBI, 8600 Rockville Pike, Rockville, MD, 20894,
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Keywords:
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Gibbs sampling ; likelihood function ; protein sequence motifs ; secondary structures ; segment overlap
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Abstract:
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Identifying common local segments, also called motifs, in multiple protein sequences plays an important role for establishing homology between proteins. Homology is easy to establish when sequences are similar. However, for distant proteins, it is much more difficult to align motifs that are not similar in sequences but still share common structures or functions. This is a first attempt to align multiple protein sequences using both primary and secondary structure information. A new sequence model is proposed so that the model assigns high probabilities not only to motifs that contain conserved amino acids but also to motifs that present common secondary structures. The proposed method is tested in a structural alignment database BAliBASE. Test results show that information brought by the predicted secondary structures greatly improves motif identification.
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- The address information is for the authors that have a + after their name.
- Authors who are presenting talks have a * after their name.
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