Abstract: The Partitioned Global Address Space (PGAS) programming
paradigm offers ease-of-use in expressing parallelism
through a global shared address space while emphasizing performance
by providing locality awareness through the partitioning of
this address space. Therefore, the interest in PGAS programming
languages is growing and many new languages have emerged and
are becoming ubiquitously available on nearly all modern parallel
architectures. Recently, new parallel machines with multiple cores
are designed for targeting high performance applications. Most of the
efforts have gone into benchmarking but there are a few examples of
real high performance applications running on multicore machines.
In this paper, we present and evaluate a parallelization technique
for implementing a local DNA sequence alignment algorithm using
a PGAS based language, UPC (Unified Parallel C) on a chip
multithreading architecture, the UltraSPARC T1.
Abstract: Biological sequences from different species are called or-thologs if they evolved from a sequence of a common ancestor species and they have the same biological function. Approximations of Kolmogorov complexity or entropy of biological sequences are already well known to be useful in extracting similarity information between such sequences -in the interest, for example, of ortholog detection. As is well known, the exact Kolmogorov complexity is not algorithmically computable. In prac-tice one can approximate it by computable compression methods. How-ever, such compression methods do not provide a good approximation to Kolmogorov complexity for short sequences. Herein is suggested a new ap-proach to overcome the problem that compression approximations may notwork well on short sequences. This approach is inspired by new, conditional computations of Kolmogorov entropy. A main contribution of the empir-ical work described shows the new set of entropy-based machine learning attributes provides good separation between positive (ortholog) and nega-tive (non-ortholog) data - better than with good, previously known alter-natives (which do not employ some means to handle short sequences well).Also empirically compared are the new entropy based attribute set and a number of other, more standard similarity attributes sets commonly used in genomic analysis. The various similarity attributes are evaluated by cross validation, through boosted decision tree induction C5.0, and by Receiver Operating Characteristic (ROC) analysis. The results point to the conclu-sion: the new, entropy based attribute set by itself is not the one giving the best prediction; however, it is the best attribute set for use in improving the other, standard attribute sets when conjoined with them.
Abstract: With the rapid development in the field of life
sciences and the flooding of genomic information, the need for faster
and scalable searching methods has become urgent. One of the
approaches that were investigated is indexing. The indexing methods
have been categorized into three categories which are the lengthbased
index algorithms, transformation-based algorithms and mixed
techniques-based algorithms. In this research, we focused on the
transformation based methods. We embedded the N-gram method
into the transformation-based method to build an inverted index
table. We then applied the parallel methods to speed up the index
building time and to reduce the overall retrieval time when querying
the genomic database. Our experiments show that the use of N-Gram
transformation algorithm is an economical solution; it saves time and
space too. The result shows that the size of the index is smaller than
the size of the dataset when the size of N-Gram is 5 and 6. The
parallel N-Gram transformation algorithm-s results indicate that the
uses of parallel programming with large dataset are promising which
can be improved further.