Dataset Information

Adaptive GDDA-BLAST: fast and efficient algorithm for protein sequence embedding.

ABSTRACT: A major computational challenge in the genomic era is annotating structure/function to the vast quantities of sequence information that is now available. This problem is illustrated by the fact that most proteins lack comprehensive annotations, even when experimental evidence exists. We previously theorized that embedded-alignment profiles (simply "alignment profiles" hereafter) provide a quantitative method that is capable of relating the structural and functional properties of proteins, as well as their evolutionary relationships. A key feature of alignment profiles lies in the interoperability of data format (e.g., alignment information, physio-chemical information, genomic information, etc.). Indeed, we have demonstrated that the Position Specific Scoring Matrices (PSSMs) are an informative M-dimension that is scored by quantitatively measuring the embedded or unmodified sequence alignments. Moreover, the information obtained from these alignments is informative, and remains so even in the "twilight zone" of sequence similarity (<25% identity). Although our previous embedding strategy was powerful, it suffered from contaminating alignments (embedded AND unmodified) and high computational costs. Herein, we describe the logic and algorithmic process for a heuristic embedding strategy named "Adaptive GDDA-BLAST." Adaptive GDDA-BLAST is, on average, up to 19 times faster than, but has similar sensitivity to our previous method. Further, data are provided to demonstrate the benefits of embedded-alignment measurements in terms of detecting structural homology in highly divergent protein sequences and isolating secondary structural elements of transmembrane and ankyrin-repeat domains. Together, these advances allow further exploration of the embedded alignment data space within sufficiently large data sets to eventually induce relevant statistical inferences. We show that sequence embedding could serve as one of the vehicles for measurement of low-identity alignments and for incorporation thereof into high-performance PSSM-based alignment profiles.

SUBMITTER: Hong Y

PROVIDER: S-EPMC2962639 | biostudies-literature | 2010 Oct

REPOSITORIES: biostudies-literature

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Publications

Adaptive GDDA-BLAST: fast and efficient algorithm for protein sequence embedding.

Hong Yoojin Y Kang Jaewoo J Lee Dongwon D van Rossum Damian B DB

PloS one 20101022 10

A major computational challenge in the genomic era is annotating structure/function to the vast quantities of sequence information that is now available. This problem is illustrated by the fact that most proteins lack comprehensive annotations, even when experimental evidence exists. We previously theorized that embedded-alignment profiles (simply "alignment profiles" hereafter) provide a quantitative method that is capable of relating the structural and functional properties of proteins, as wel ...[more]

PMID: 21042584

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Project description:Purpose: The purpose of this work was to propose an online replanning algorithm, named intensity field projection (IFP), that directly adjusts intensity distributions for each beam based on the deformation of structures. IFP can be implemented within a reasonably acceptable time frame. Methods and Materials: The online replanning method is based on the gradient-based free form deformation (GFFD) algorithm, which we have previously proposed. The method involves the following steps: The planning computed tomography (CT) and cone-beam CT image are registered to generate a three-dimensional (3-D) deformation field. According to the 3-D deformation field, the registered image and a new delineation are generated. The two-dimensional (2-D) deformation field of ray intensity in each beam direction is determined based on the 3-D deformation field in the region of interest. The 2-D ray intensity distribution in the corresponding beam direction is deformed to generate a new 2-D ray intensity distribution. According to the new 2-D ray intensity distribution, corresponding multi-leaf collimator (MLC), and jaw motion data are generated. The feasibility and advantages of our method have been demonstrated in 20 lung cancer intensity modulated radiation therapy (IMRT) cases. Results: Substantial underdosing in the CTV is seen in the original and the repositioning plans. The average prescription dose coverage (V100%) and D95 for CTV were 100% and 60.3 Gy for the IFP plans compared to 82.6% (P < 0.01) and 44.0 Gy (P < 0.01) for original plans, 86.7% (P < 0.01), and 58.5 Gy (P < 0.01) for repositioning plans. On average, the mean total lung doses were 12.2 Gy for the IFP plan compared to the 12.4 Gy (P < 0.01) and 12.6 Gy (P < 0.01) for the original and the repositioning plans. The entire process of IFP can be completed within 3 min. Conclusions: We proposed an online replanning strategy for automatically correcting interfractional anatomy variations. The preliminary results indicate that the IFP method substantially increased planning speed for online adaptive replanning.

Dataset Information

Adaptive GDDA-BLAST: fast and efficient algorithm for protein sequence embedding.

Publications

Adaptive GDDA-BLAST: fast and efficient algorithm for protein sequence embedding.

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