TY - JOUR
T1 - Improvement in protein sequence-structure alignment using insertion/deletion frequency arrays.
AU - Ellrott, Kyle
AU - Guo, Jun tao
AU - Olman, Victor
AU - Xu, Ying
PY - 2007
Y1 - 2007
N2 - As a protein evolves, not every part of the amino acid sequence has an equal probability of being deleted or for allowing insertions, because not every amino acid plays an equally important role in maintaining the protein structure. However the most prevalent models in fold recognition methods treat every amino acid deletion and insertion as equally probable events. We have analyzed the alignment patterns for homologous and analogous sequences to determine patterns of insertion and deletions, and used that information to determine the statistics of insertions and deletions for different amino acids of a target sequence. We define these patterns as Insertion/Deletion (Indel) Frequency Arrays (IFA). By applying IFA to the protein threading problem, we have been able to improve the alignment accuracy, especially for proteins with low sequence identity.
AB - As a protein evolves, not every part of the amino acid sequence has an equal probability of being deleted or for allowing insertions, because not every amino acid plays an equally important role in maintaining the protein structure. However the most prevalent models in fold recognition methods treat every amino acid deletion and insertion as equally probable events. We have analyzed the alignment patterns for homologous and analogous sequences to determine patterns of insertion and deletions, and used that information to determine the statistics of insertions and deletions for different amino acids of a target sequence. We define these patterns as Insertion/Deletion (Indel) Frequency Arrays (IFA). By applying IFA to the protein threading problem, we have been able to improve the alignment accuracy, especially for proteins with low sequence identity.
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U2 - 10.1142/9781860948732_0034
DO - 10.1142/9781860948732_0034
M3 - Article
C2 - 17951836
AN - SCOPUS:38449088265
SN - 1752-7791
VL - 6
SP - 335
EP - 342
JO - Computational systems bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference
JF - Computational systems bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference
ER -