Accelerating calculations of RNA secondary structure partition functions using GPUs

Table 1 Biological RNA sequences examined ^*

Sequence	# bases	Reference
tRNA RQ2640	75	[28]
tRNA RD0500	76	[28]
tRNA RA7680	76	[28]
tRNA RD0260	77	[28]
tRNA RR1664	77	[28]
Candida albicans 5S rRNA	114	[29]
Escherichia coli 5S rRNA	120	[30]
P546 folding domain of Tetrahymenathermophilia group I intron	155	[31]
Bacillus stearothermophilus SRP RNA	268	[32]
3’ UTR of Bombyx mori R2 element with flanking vector sequence	300	[33]
Tetrahymena thermophilia group I intron	433	[30]
Saccharomyces cerevisiae A5 group II intron	632	[34]
Escherichia coli small subunit rRNA	1542	[30]
Escherichia coli large subunit rRNA	2904	[29]
human ICAM-1 mRNA	2986	[35]
HIV-1 NL43 genome (GenBank: AF324493)	9709	[36]

ISSN: 1748-7188