SIMPLE ALIGNMENT CONSTRAINTS FOR EFFICIENT ALIGNMENT OF RNA SEQUENCES USING FAMILY-SPECIFIC MODELS Conference Paper

abstract

• In this extended abstract, we present a simple method for finding alignment constraints that can be used for efficient alignment of RNAs based on family-specific models, such as profile context-sensitive HMMs (profile-csHMMs) and covariance models (CMs). The alignment constraints are established based on the alignment positions predicted by a profile-HMM. Application of the proposed constraints to the profile-csHMM based structural RNA alignment method significantly improved the average alignment speed without degrading the alignment accuracy.

name of conference

• 2009 IEEE International Workshop on Genomic Signal Processing and Statistics

authors

• Yoon, Byung-Jun

published proceedings

• 2009 IEEE International Workshop on Genomic Signal Processing and Statistics

author list (cited authors)

• Yoon, B.

citation count

• 0

complete list of authors

• Yoon, Byung-Jun

publication date

• January 2009

publisher

• Institute of Electrical and Electronics Engineers (IEEE)  Publisher

keywords

• Biotechnology
• Genetics
• Human Genome

Digital Object Identifier (DOI)

• 10.1109/gensips.2009.5174323

International Standard Book Number (ISBN) 13

• 9781424447619

start page

• 1

end page

• 3

URL

• http%3A%2F%2Fdx.doi.org%2F10.1109%2Fgensips.2009.5174323