TY - GEN
T1 - Designing autocorrelated genes
AU - Yeasmin, Rukhsana
AU - Tithi, Jesmin Jahan
AU - Chen, Jeffrey
AU - Skiena, Steven
PY - 2013
Y1 - 2013
N2 - The redundancy in the genetic code enables a protein to be encoded by many different sequences. Recent studies show that the degree of tRNA autocorrelation in a coding sequence has important effects on translation speed. The tRNA pairing index (TPI) has been used widely to study the phenomenon of autocorrelation in sequences. However TPI only counts successive transitions of tRNA usage, with- out regard to how far apart they occur in the sequence. In this paper, we propose a new type of autocorrelation measure, DICA (Distance Incorporated Codon Autocorre- lation), which weighs positional distance between codons as well as the number of transitions. We demonstrate that our DICA correlates better to the expression level of a particular gene than TPI. Finally, we devise exact and heuristic algorithms to find near optimally autocorrelated and anti- Autocorrelated genes for the purposes of synthetic gene design.
AB - The redundancy in the genetic code enables a protein to be encoded by many different sequences. Recent studies show that the degree of tRNA autocorrelation in a coding sequence has important effects on translation speed. The tRNA pairing index (TPI) has been used widely to study the phenomenon of autocorrelation in sequences. However TPI only counts successive transitions of tRNA usage, with- out regard to how far apart they occur in the sequence. In this paper, we propose a new type of autocorrelation measure, DICA (Distance Incorporated Codon Autocorre- lation), which weighs positional distance between codons as well as the number of transitions. We demonstrate that our DICA correlates better to the expression level of a particular gene than TPI. Finally, we devise exact and heuristic algorithms to find near optimally autocorrelated and anti- Autocorrelated genes for the purposes of synthetic gene design.
KW - Codon autocorrelation
KW - Gene design
KW - Sequence analysis
UR - https://www.scopus.com/pages/publications/84888165980
U2 - 10.1145/2506583.2506604
DO - 10.1145/2506583.2506604
M3 - Conference contribution
AN - SCOPUS:84888165980
SN - 9781450324342
T3 - 2013 ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM-BCB 2013
SP - 458
EP - 467
BT - 2013 ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM-BCB 2013
T2 - 2013 4th ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM-BCB 2013
Y2 - 22 September 2013 through 25 September 2013
ER -