UNIVERSAL SELF SCORER BIOLOGY PDF

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This figure shows the scoring process of the first three elements. The yellow color indicates the bases that are being considered. The red color indicates the highest possible score for the cell being scored. Initialization of the scoring matrix left 1 and the scoring process of the first three elements left The finished scoring matrix is shown below on the left.

The blue color shows the highest score. An element can receive score from more than one element, each will form a different path if this element is traced back. In case of multiple highest scores, traceback should be done starting with each highest score.

The traceback process is shown below on the right. The best local alignment is generated in the reverse direction. This implementation includes Altivec accelerated code for PowerPC G4 and G5 processors that speeds up comparisons 10—fold, using a modification of the Wozniak, approach, [12] and an SSE2 vectorization developed by Farrar [13] making optimal protein sequence database searches quite practical.

However the same tests running on dual NVidia GeForce GTX cards are almost twice as fast as the Farrar implementation for all sequence sizes tested. The company Sencel Bioinformatics has applied for a patent covering this approach.

Sencel is developing the software further and provides executables for academic use free of charge. Danish bioinformatics company CLC bio has achieved speed-ups of close to over standard software implementations with SSE2 on an Intel 2. Performance benchmarks of this software package show up to 10 fold speed acceleration relative to standard software implementation on the same processor.

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This figure shows the scoring process of the first three elements. The yellow color indicates the bases that are being considered. The red color indicates the highest possible score for the cell being scored. Initialization of the scoring matrix left 1 and the scoring process of the first three elements left The finished scoring matrix is shown below on the left. The blue color shows the highest score.

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