BMC Bioinformatics

Table 2 The maximum sequence length depending on the GPU RAM and window size parameter

From: Protein alignment algorithms with an efficient backtracking routine on multiple GPUs

*window size*	6 GB	4 GB	2 GB	1 GB	512 MB
16	7036	5721	3994	2751	1836
32	3518	2860	1996	1374	916
48	2345	1906	1330	915	609
64	1758	1429	997	685	455
80	1406	1143	796	547	362
96	1171	951	663	454	300
112	1003	815	567	388	255
128	877	712	495	338	221
144	779	633	439	299	194
160	701	569	394	268	172
176	637	516	358	242	155
192	583	473	327	220	139
208	538	436	301	202	126
224	499	404	278	186	115
240	465	376	259	172	105

Estimated length of the sequences that can be processed by the algorithm depending on the amount of the global memory (GPU RAM) and the window size parameter.

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ISSN: 1471-2105

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