Browsing by Subject "Gene mapping."

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Open Access
Massively parallel mapping of next generation sequence reads using GPU
(2012) Korkmaz, Mustafa
The high throughput sequencing (HTS) methods have already started to fundamentally revolutionize the area of genome research through low-cost and highthroughput genome sequencing. However, the sheer size of data imposes various computational challenges. For example, in the Illumina HiSeq2000, each run produces over 7-8 billion short reads and over 600 Gb of base pairs of sequence data within less than 10 days. For most applications, analysis of HTS data starts with read mapping, i.e. nding the locations of these short sequence reads in a reference genome assembly. The similarities between two sequences can be determined by computing their optimal global alignments using a dynamic programming method called the Needleman-Wunsch algorithm. The Needleman-Wunsch algorithm is widely used in hash-based DNA read mapping algorithms because of its guaranteed sensitivity. However, the quadratic time complexity of this algorithm makes it highly timeconsuming and the main bottleneck in analysis. In addition to this drawback, the short length of reads ( 100 base pairs) and the large size of mammalian genomes (3.1 Gbp for human) worsens the situation by requiring several hundreds to tens of thousands of Needleman-Wunsch calculations per read. The fastest approach proposed so far avoids Needleman-Wunsch and maps the data described above in 70 CPU days with lower sensitivity. More sensitive mapping approaches are even slower. We propose that e cient parallel implementations of string comparison will dramatically improve the running time of this process. With this motivation, we propose to develop enhanced algorithms to exploit the parallel architecture of GPUs.
Open Access
Modeling of flexible needle insertion in moving tissue
(2012) Güven, Aslı Deniz
Steerable needles can be used for minimally invasive surgeries to reach clinical targets which were previously inaccessible by rigid needles. Using such flexible needles to plan an insertion for these procedures is difficult because of the nonholonomic motion of the bevel-tip needles and the presence of anatomical obstacles. In this work, we take into consideration another property of such procedures being the tissue motion as well as these. For instance in a minimally invasive cardiac surgery one should take into account the effect of the heart’s beating motion on the needle during its insertion or in any other procedure the effect of human breathing. In this thesis, we develop a motion model for a bevel-tip needle such that it can be inserted within in any tissue under a motion which can be characterized by a time-dependent diffeomorphism. We then explore motion planning under periodic motion of a homogeneous, planar tissue where we use the Rapidly-exploring Random Trees (RRTs) method with the developed model to explore the tissue. While we perform the planning, we aim that the needle reaches a target area in the tissue while avoiding obstacles which are actually tissue segments that we want to avoid getting in contact with and intuitively follow the same motion of the tissue.