Multiple Sequence Alignment and its Applications
Multiple sequence alignment of protein or DNA sequences is one of the
most fundamental problems in computational biology. It is an alignment
of three or more sequences. It is widely used in many applications
such as phylogenetic analysis and identification of conserved motifs.
This project aims to
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Find biologically relevant alignments by considering not only
the sequence of letters, but also the additional structural
information such as secondary structure elements.
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Given a meaningful scoring function, optimize the alignment of
the input sequences according to this function.
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Explore new biology applications that make use of multiple
sequences.
Software
The QOMA code can be downloaded from here.
People
Publications
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Xu Zhang, Tamer Kahveci,
QOMA2: Optimizing the alignment
of many sequences,
BIBE, 2007. (Abstract)
(PDF)
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Xu Zhang, Tamer Kahveci,
Quasi-Optimal Multiple Alignment
of Protein Sequences,
Bioinformatics, 23(2): 162-168
(2007). (PubMed)
(Bioinformatics)
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Xu Zhang, Tamer Kahveci
A New Approach for Alignment of
Multiple Proteins,
PSB, 2006, pages 339-350. (Abstract)
(PDF)
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Yue Li, Lan Luo, Tao Li and Tamer Kahveci,
Microarchitecture
Characteristics and Implications of Alignment of Multiple
Bioinformatics Sequences,
Workshop on Unique Chips and Systems
(Held in conjunction with IEEE ISPASS), 2006.
Tamer Kahveci
Last modified: Sat Oct 6 07:22:36 EDT 2007