CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment.

BACKGROUND: Searching for similarities in protein and DNA databases has become a routine procedure in Molecular Biology. The Smith-Waterman algorithm has been available for more than 25 years. It is based on a dynamic programming approach that explores all the possible alignments between two sequences; as a result it returns the optimal local alignment. Unfortunately, the computational cost is very high, requiring a number of operations proportional to the product of the length of two sequences. Furthermore, the exponential growth of protein and DNA databases makes the Smith-Waterman algorithm unrealistic for searching similarities in large sets of sequences. For these reasons heuristic approaches such as those implemented in FASTA and BLAST tend to be preferred, allowing faster execution times at the cost of reduced sensitivity. The main motivation of our work is to exploit the huge computational power of commonly available graphic cards, to develop high performance solutions for sequence alignment. RESULTS: In this paper we present what we believe is the fastest solution of the exact Smith-Waterman algorithm running on commodity hardware. It is implemented in the recently released CUDA programming environment by NVidia. CUDA allows direct access to the hardware primitives of the last-generation Graphics Processing Units (GPU) G80. Speeds of more than 3.5 GCUPS (Giga Cell Updates Per Second) are achieved on a workstation running two GeForce 8800 GTX. Exhaustive tests have been done to compare our implementation to SSEARCH and BLAST, running on a 3 GHz Intel Pentium IV processor. Our solution was also compared to a recently published GPU implementation and to a Single Instruction Multiple Data (SIMD) solution. These tests show that our implementation performs from 2 to 30 times faster than any other previous attempt available on commodity hardware. CONCLUSIONS: The results show that graphic cards are now sufficiently advanced to be used as efficient hardware accelerators for sequence alignment. Their performance is better than any alternative available on commodity hardware platforms. The solution presented in this paper allows large scale alignments to be performed at low cost, using the exact Smith-Waterman algorithm instead of the largely adopted heuristic approaches.

Reactions of chicken biliary immunoglobulin A with avian mycoplasmas.

Chicken bile was examined for mycoplasma by culture and for antibody against mycoplasma by indirect immunoperoxidase assay (IIPA) detecting chicken either IgA or IgG and IgM, as well as by rapid plate agglutination (RPA), haemagglutination-inhibition (HI) and double immuno-diffusion (DID). Cultures indicated the presence of M. gallisepticum (Mg) and Ai. synoviae (Ms) in bile and their isolations were positively correlated with those from upper respiratory tract. In 45 chickens from five flocks examination of biliary samples with IIPA detected considerably higher rates of Mg and Ms antibodies than the same assay performed with sera especially those of IgA class of antibody. In chickens with a strong serological response to Mg, titres of specific agglutinins and HI antibody in biliary samples were significantly higher than those found in sera. Only biliary fractions containing Ig exhibited antibody activity.

Humoral and local antibodies in chickens with mixed infection with three Mycoplasma species.

Eight one-year-old commercial layer hens with strong humoral antibody response to Mycoplasma synoviae were examined for mycoplasmas. Cultures from the respiratory tract, the Harderian gland and the oviduct showed the group to be infected with M. synoviae, M. gallisepticum, M. gallinarum and Bordetella avium. The humoral antibody response to M. synoviae was strongly positive and supported by high titre specific IgG and IgM class antibody, while that against M. gallisepticum and M. gallinarum was weak or undetectable. However, an antibody response to M. gallisepticum and M. gallinarum was demonstrated in the Harderian gland, respiratory secretions and oviduct of some birds along with antibody to M. synoviae. In contrast with serum, antibodies of IgA and IgG classes against M. gallisepticum were observed in the extracts of spleen of all birds. These data indicate that adult chickens are capable of mounting an antibody response against at least three Mycoplasma species during a mixed infection but it may be necessary to examine tissues as well as serum to demonstrate them.