TY - GEN
T1 - Time-frequency based biological sequence querying
AU - Ravichandran, L.
AU - Papandreou-Suppappola, Antonia
AU - Spanias, Andreas
AU - Lacroix, Z.
AU - Legendre, C.
PY - 2010/11/8
Y1 - 2010/11/8
N2 - We investigate the use of time-frequency (TF) methods to query biological sequences in search of regions of similarity or critical relationships among the sequences. Existing querying approaches are insensitive to repeats, especially in low-complexity regions, and do not provide much support for efficiently querying sub-sequences with inserts and deletes (or gaps). Our approach uses highly-localized basis functions and multiple transformations in the TF plane to map characters in a sequence as well as different properties of a sub-sequence, such as its position in the sequence or number of gaps between sub-sequences. We analyze gapped query-based alignment methods using transformations in the TF plane while demonstrating the method's possible operation in real-time without pre-processing. The algorithm's performance is compared to the widely-accepted BLAST alignment approach, and a significance improvement is observed for queries with repetitive segments.
AB - We investigate the use of time-frequency (TF) methods to query biological sequences in search of regions of similarity or critical relationships among the sequences. Existing querying approaches are insensitive to repeats, especially in low-complexity regions, and do not provide much support for efficiently querying sub-sequences with inserts and deletes (or gaps). Our approach uses highly-localized basis functions and multiple transformations in the TF plane to map characters in a sequence as well as different properties of a sub-sequence, such as its position in the sequence or number of gaps between sub-sequences. We analyze gapped query-based alignment methods using transformations in the TF plane while demonstrating the method's possible operation in real-time without pre-processing. The algorithm's performance is compared to the widely-accepted BLAST alignment approach, and a significance improvement is observed for queries with repetitive segments.
KW - Biological sequence querying
KW - Gapped local alignment
KW - Metaplectic transformations
KW - Time-frequency methods
UR - http://www.scopus.com/inward/record.url?scp=78049401904&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=78049401904&partnerID=8YFLogxK
U2 - 10.1109/ICASSP.2010.5495708
DO - 10.1109/ICASSP.2010.5495708
M3 - Conference contribution
AN - SCOPUS:78049401904
SN - 9781424442966
T3 - ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings
SP - 4174
EP - 4177
BT - 2010 IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2010 - Proceedings
T2 - 2010 IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2010
Y2 - 14 March 2010 through 19 March 2010
ER -