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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

CORRTEX Analysis Techniques

Continuous Reflectometry for Radius versus Time Experiments, or CORRTEX, is a diagnostic that was developed during nuclear testing to measure the distance at which rock walls were disrupted by an explosive device as a function of the time at which disruption occurred. Distances recorded are dynamic measurements of cable length as the shockwaves from an explosive event crush the experiment cables, reducing their usable length. Applications of the CORRTEX diagnostic have been expanded in recent times to include instrumentation of the explosive device itself, to record phenomena such as the speed of the detonation wave in the explosive charge and the crushing or disassembly of material in the charge housing. The diagnostic has likewise been used to monitor explosive performance in rock blasting and oil well hole-clearing activities.

42 ENGINEERING↗
DOE OSTI2019

Measurements of Hydrogen Generation Rates using a Sealed Reactor System - 19428

Sealed reactor tests were performed to measure the hydrogen generation rate (HGR) from stored radioactive waste at the Savannah River Site. HGR may be very low, on the order of 7.5 x 10{sup -13} (m{sup 3}/h)/L [that is, cubic meters of H{sub 2} generated per hour per liter of radioactive liquid waste, or 10{sup -10} (ft{sup 3}/h)/gal]. Because the estimated HGR limit of detection for an open, continuous flow, system is approximately 7.5 x 10{sup -10} (m{sup 3}/h)/L [or 10{sup -7} (ft{sup 3}/h)/gal], a more sensitive method was needed. By accumulating generated gasses in a sealed system without a continuous purge gas, the resulting concentrations can increase the sensitivity of measurement, which is based on time of heating. In 2017, Savannah River Remediation declared a Potential Inadequacy in the Safety Analysis related to the potential thermal decomposition of organics that generate hydrogen in each of three Liquid Waste facilities: Concentration, Storage and Transfer Facility, Saltstone Production Facility, and the Defense Waste Processing Facility. The research for this study concerns low activity waste of Tank 50, which feeds the Saltstone Production Facility. This study evaluated the impact of organics including formate on the generation of H{sub 2}. Samples of SRS Tank 50 waste, which is a nominal 5 molar sodium salt solution, were sealed in stainless steel reactors and held at varying temperatures, e.g., 50 deg. C, 75 deg. C, 100 deg. C, and 120 deg. C, to determine if organic compounds are decomposing into H2. The experiments included trace solids used to stabilize waste in grout, e.g., grout-premix and Blast Furnace Slag, to determine if any solid phase reactions are present, which would accelerate or inhibit the generation of H{sub 2} at these temperatures. This paper describes the sealed reactors designed and constructed at Savannah River National Laboratory and the radioactive tests that were performed to measure HGR in both oxic and anoxic atmospheres. The shakedown tests showed the sealed reactors to be leak tight and hydrogen concentrations from calibrated standards could be accurately measured. Previous simulant tests helped to perfect the test methods and better design the radioactive tests. The radioactive results showed that the rate of hydrogen generated from Tank 50 waste, over a range of temperatures from 30 deg. C up to 120 deg. C, is bounded by an empirical relation (Hu Equation) that can be used to approximate HGRs in Tank 50 radioactive waste. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2016

Moment tensor analysis of very shallow sources

An issue for moment tensor (MT) inversion of shallow seismic sources is that some components of the Green’s functions have vanishing amplitudes at the free surface, which can result in bias in the MT solution. The effects of the free surface on the stability of the MT method become important as we continue to investigate and improve the capabilities of regional full MT inversion for source–type identification and discrimination. It is important to understand free–surface effects on discriminating shallow explosive sources for nuclear monitoring purposes. It may also be important in natural systems that have very shallow seismicity, such as volcanic and geothermal systems. We examine the effects of the free surface on the MT via synthetic testing and apply the MT–based discrimination method to three quarry blasts from the HUMMING ALBATROSS experiment. These shallow chemical explosions at ~10 m depth and recorded up to several kilometers distance represent rather severe source–station geometry in terms of free–surface effects. We show that the method is capable of recovering a predominantly explosive source mechanism, and the combined waveform and first–motion method enables the unique discrimination of these events. Furthermore, recovering the design yield using seismic moment estimates from MT inversion remains challenging, but we can begin to put error bounds on our moment estimates using the network sensitivity solution technique.

58 GEOSCIENCES↗
NASA NTRS1991

An infrared analysis of Puppis A

A quantitative analysis of the infrared emission of the supernova remnant (SNR) Puppis A as seen by the Infrared Astronomical Satellite is presented. Physical parameters of the remnant (and the surrounding interstellar medium), including density, mass, temperature, and age are estimated. The infrared spectrum of Puppis A is fit by models of thermal emission from interstellar dust grains which have been swept up into the SNR where they are collisionally heated by the shocked gas. Evidence of an enhanced abundance of very small grains in the interstellar medium near Puppis A, and evidence of their destruction by the advancing blast wave, are found.

Arendt, Richard G.↗
DOE OSTI2016

New Formulation of Cast Stone for {sup 99}Tc Immobilization in Sulfate Rich Secondary Waste Stream - 16098

A low-temperature, cementitious waste form called Cast Stone (or grout) has been selected for solidification of the Effluent Treatment Facility (ETF)-treated wastes at the Hanford Site. Because the waste stream to be solidified may be relatively high in sulfate, the current Cast Stone dry blend formulation with ordinary Portland cement (OPC), fly ash (FA), and blast furnace slag (BFS) (47% BFS, 45% FA, and 8% OPC) may not be adequate. Thus a new formulation, called secondary waste grout, was proposed and tested. The secondary waste grout uses hydrated lime [Ca(OH){sub 2}] to tie up the sulfate initially such that ettringite [Ca{sub 6}Al{sub 2}(SO{sub 4}){sub 3}(OH){sub 12}.26(H{sub 2}O)] forms rapidly instead of forming as the cementitious waste form cures. Three different liquid waste simulants (242-A evaporator, Environmental Restoration Disposal Facility [ERDF] leachates, and Hanford Tank Waste Treatment and Immobilization Plant [WTP] off-gas condensates) were prepared and solidified using this new dry blend formulation. Baseline grout dry mixes were 20 wt% hydrated lime (HL), 35 wt% OPC, and 45 wt% BFS, and two different water-to-dry mix (w/dm) ratios (0.5 and 0.6) of free water mass to mass of dry blend were tested. After curing for a minimum of 28 days, the grout solidified waste forms were characterized and used for Tc leachability testing using the EPA 1315 Method. X-ray diffraction analysis confirmed that ∼12-15% of ettringite was formed in early stage of 28-day curing for the grouts prepared with the high sulfate WTP simulant and HL addition. In addition, the new formulation of secondary waste grout prepared with HL (20%), OPC (35%), and BFS (45%) at either 0.5 or 0.6 water to dry mix ratio yields higher average Tc interval leachability index (LI) values (12.5 to 13.9) after 28 to 90 days of leaching using deionized water, which is higher than the desired {sup 99}Tc LI value of 12 for grout destined for burial in the Integrated Disposal Facility at the Hanford Site. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2010

BLAST OBSERVATIONS OF THE SOUTH ECLIPTIC POLE FIELD: NUMBER COUNTS AND SOURCE CATALOGS

We present results from a survey carried out by the Balloon-borne Large Aperture Submillimeter Telescope (BLAST) on a 9 deg{sup 2} field near the South Ecliptic Pole at 250, 350, and 500 {mu}m. The median 1{sigma} depths of the maps are 36.0, 26.4, and 18.4 mJy, respectively. We apply a statistical method to estimate submillimeter galaxy number counts and find that they are in agreement with other measurements made with the same instrument and with the more recent results from Herschel/SPIRE. Thanks to the large field observed, the new measurements give additional constraints on the bright end of the counts. We identify 132, 89, and 61 sources with S/N {>=}4 at 250, 350, 500 {mu}m, respectively and provide a multi-wavelength combined catalog of 232 sources with a significance {>=}4{sigma} in at least one BLAST band. The new BLAST maps and catalogs are available publicly at http://blastexperiment.info.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS2005

X-Ray Emission from "Uranium" Stars

The project aims to secure XMM observations of two targets with extremely low abundances of the majority of heavy elements (e.g., log[Fe/H] $\sim$-4), but that show absorption lines of uranium. The presence of an r-process element such as uranium requires a binary star system in which the companion underwent a supernova explosion. A binary star system raises the distinct possibility of the existence of a compact object, most likely a neutron star, in the binary, assuming it survived the supernova blast. The presence of a compact object then suggests X-ray emission if sufficient matter accretes to the compact object. The observations were completed less than one year ago following a series of reobservations to correct for significant flaring that occurred during the original observations. The ROSAT all-sky survey was used to report on the initial assessment of X-ray emission from these objects; only upper limits were reported. These upper limits were used to justify the XMM observing time, but with the expectation that upper limits would merely be pushed lower. The data analysis hinges critically on the quality and degree of precision with which the background is handled. During the past year, I have spent some time learning the ins and outs of XMM data analysis. In the coming year, I can apply that learning to the analysis of the 'uranium' stars.

Schlegel, Eric↗
NASA NTRS2010

Analysis of a Hypergolic Propellant Explosion During Processing of Launch Vehicles in the VAB

NASA is developing launch vehicles to support missions to Low Earth Orbit (LEO), the moon and deep space. Whether manned or unmanned, the vehicle components will likely be integrated in the Vehicle Assembly Building (VAB) at Kennedy Space Center (KSC) and typically include a fueled spacecraft (SC) that sits on top of one or more stages. The processing of a fueled SC involves hazardous operations when it is brought into the VAB Transfer Aisle and lifted a significant height for mating with lower stages. Accidents resulting from these hazardous operations could impact unrelated personnel working in buildings adjacent to the VAB. Safe separation distances based on the DOD Explosives Standards Quantity-Distance (Q-D) approach result in large IBD arcs. This paper presents site-specific air blast and fragmentation hazard analyses for comparison with the Q-D arcs as well as consequence and risk analyses to provide added information for the decision maker. A new physics-based fragmentation model is presented that includes: a) the development of a primary fragment list (which defines the fragment characteristics) associated with a hypergolic propellant explosion, b) a description of a 3D fragment bounce model, c) the results of probabilistic Monte-Carlo simulations (that include uncertainties in the fragment characteristics) to determine: i) the hazardous fragment density distance, ii) the expected number of wall/roof impacts and penetrations to over 40 buildings adjacent to the VAB, and iii) the risk to building occupants.

Chrostowski, Jon D.↗
DOE OSTI2012

Crystal structure of an eIF4G-like protein from Danio rerio

The gene LOC 91917 Danio rerio (zebrafish) encodes a protein annotated in the UniProt knowledgebase as the middle domain of eukaryotic initiation factor 4G domain containing protein b (MIF4Gdb). Its molecular weight is 25.8 kDa, and it comprises 222 amino acid residues. BLAST searches revealed homologues of D. rerio MIF4Gdb in many eukaryotes including humans. The homologue sand MIF4Gdb were identified as members of the Pfam family, MIF4G (PF2854), which is named after the middle domain of eukaryotic initiation factor 4G (eIF4G). eIF4G is a component of eukaryotic translational initiation complex, and contains binding sites for other initiation factors, suggesting its critical role in translational initiation. The MIF4G domain also occurs in several other proteins involved in RNA metabolism, including the Nonsense-mediated mRNA decay 2 protein (NMD2/UPF2), and the nuclear cap-binding protein 80-kDa subunit (CBP80). Sequence and structure analysis of the MIF4G domains in many proteins indicate that the domain assumes an all helical fold and has tandem repeated motifs. The zebrafish protein described here has homology to domains of other proteins variously referred to as NIC-containing proteins (NMD2, eIF4G, CBP80). The biological function of D. rerio MIF4Gdb has not yet been experimentally characterized, and the annotation is based on amino acid sequence comparison. D. rerio MIF4Gdb did not share more than 25% sequence identity with any protein for which the three-dimensional structure is known and was selected as a target for structure determination by the Center for Eukaryotic Structural Genomics (CESG). Here, they report the crystal structure of D. rerio MIF4Gdb (UniGene code Dr.79360, UniProt code Q5EAQ1, CESG target number GO.79294).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Measurements of Picosecond Energy Equilibration in Isochorically Heated Materials

In this Final Report we present the results of our DOE/FES-sponsored research on rapidly heated materials. The research focused on the details of picosecond energy equilibration and material response to isochoric heating by relativistic (or “hot”) electrons. The major goal was to improve the understanding of these processes by making time-resolved extreme ultraviolet (XUV) measurements of ultrafast energy deposition and blast-wave formation for testing impulsive-heating models in extreme thermodynamic conditions. Major achievements of the project include the design, fabrication, deployment, and use of two XUV spectrometers on the Multi-Terawatt (MTW) Laser System at the University of Rochester’s Laboratory for Laser Energetics. One of the spectrometers is coupled to an x-ray charge-coupled device (CCD) for time-integrated measurements; the other is coupled to an ultrafast x-ray streak camera for time-resolved measurements. Working together, these instruments provide absolutely calibrated data on the emitted XUV spectrum from an isochoric heated target. The new diagnostic system was used to measure and infer the time-resolved rear-surface temperature and density for different target materials and different target-interaction conditions. Experiments with laser-heated metal foils measured the ultrafast dynamics and energy deposition from hot electrons into plasma heating and blast-wave formation. The blast wave was observed emerging from the rear surface of the laser-irradiated target. The time between the prompt emission (electron-driven x-ray emission) and the blast-wave arrival was used to estimate the energy deposition into the wave. The data are consistent with a Sedov–Taylor blast wave, with energy transfer from the laser to the blast of up to 20 mJ. The data represent the first quantitative assessment of the blast-wave energy in a metal following heating by a short burst of high-intensity laser-generated hot electrons. The funding from this grant provided significant opportunities for training and professional development. The grant supported or partially supported a graduate student, a postdoctoral research associate, and a senior staff scientist. This support included bringing together a dedicated group of individuals with a niche set of experimental and theoretical skills for studying advanced material properties experiments and ultrafast radiation conditions. The team dynamic fostered training and knowledge transfer across the whole spectrum of research activities through shared experiences in advanced laboratory techniques, data analysis, modeling, and the development of new ideas, techniques, presentations, and publications. The results of this work, which significantly improve the understanding of rapid energy deposition in solid matter, have been widely disseminated to communities of interest through invited talks, contributed talks, and peer-reviewed journals.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
NASA NTRS2017

Command and Control System Software Development

Kennedy Space Center has been the heart of human space flight for decades. From the Apollo Program to the Space Shuttle Program, and now to the coming Space Launch System (SLS) and Orion, NASA will be a leader in deep space exploration for mankind. Before any rockets blast off, there is significant work to be done in preparation for launch. People working on all aspects of spaceflight must contribute by developing new technology that has yet to participate in a successful launch, and which can work with technology already proven in flight. These innovations, whether hardware or software, must be tried and true, and includes the projects to which interns contribute to. For this internship, the objective was to create a data recording system for the developers of a LCS section that records certain messages in the traffic of the system. Developers would then be able to use these recordings for analysis later on, either manually or by an automated test. The tool would be of convenience to a developer as it would be used if the system's main data recorder was not available for tests.

Velasquez, Ricky↗
NASA NTRS2018

Monitoring Astronaut Health with DNA Sequencing

In recent years microbe a plethora of microbe populations have been identified onboard the ISS (International Space Station). Approaches for real-time tracking of microbes for routine housekeeping and food/water safety monitoring will be critical for mission safety and crew health on future longer duration missions to the Moon or Mars. This work is a proof-of-concept study demonstrating an end-to-end phylogenetic identification and full genome sequencing effort of multiple microbial populations. Our methodology utilized the ISS flight-certified WetLab-2 molecular toolbox and the Biomolecule Sequencer projects for real-time end-to-end on-orbit microbial biological samples processing and molecular analysis with real time results generated utilizing only field "offline" analytic software. For this experiment we colony-cultured several ISS isolated microorganisms before generation of the pre-sequencing library via the automated VolTRAX device which enabled high library turnover with little wet-bench activity or potential future costly astronaut time. The pre-sequencing library is diluted in loading buffer and injected into the MinION sample port, drawn into the nanopore window by capillary action, and sequenced using the MinKnown. 16S and full genome alignment, nucleotide matching, gene identification, and phylogenetic sorting was accomplished utilizing the Epi2me software and the offline NCBI Blast viral, microbiome, and human somatic databases. In short, the methodologies developed herein replace the myriad of specific, often highly targeted microbiological tests used in the clinical laboratory, which would be difficult if not impossible to currently implement aboard the ISS or in deep space, with a single metagenomics test.

genomics↗
DOE OSTI2013

Metallic surfaces decontamination by using laser light

Metal surface cleaning appears to be one of the major priorities for industries especially for nuclear industries. The research and the development of a new technology that is able to meet the actual requirements (i.e. waste volume minimization, liquid effluents and chemicals free process...) seems to be the main commitment. Currently, a wide panel of technologies already exists (e.g. blasting, disk sander, electro-decontamination...) but for some of them, the efficiency is limited (e.g, Dry Ice blasting) and for others, the wastes production (liquid and/or solid) remains an important issue. One answer could be the use of a LASER light process. Since a couple of years, the Clean- Up Business Unit of the AREVA group investigates this decontamination technology. Many tests have been already performed in inactive (i.e. on simulants such as paints, inks, resins, metallic oxides) or active conditions (i.e. pieces covered with a thick metallic oxide layer and metallic pieces covered with grease). The paper will describe the results obtained in term of decontamination efficiency during all our validation process. Metallographic characterizations (i.e. SEM, X-ray scattering) and radiological analysis will be provided. We will also focus our paper on the future deployment of the LASER technology and its commercial use at La Hague reprocessing facility in 2013. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2022

Distances to Prompt Effects for a Nuclear Device

In 2010, nuclear weapon effects experts at Sandia National Laboratories (SNL) were asked to provide a quick reference document containing estimated prompt nuclear effects. This report is an update to the 2010 document that includes updated model assumptions. This report addresses only the prompt effects associated with a nuclear detonation (e.g., blast, thermal fluence, and prompt ionizing radiation). The potential medium- and longer-term health effects associated with nuclear fallout are not considered in this report because, in part, of the impracticality of making generic estimates given the high dependency of fallout predictions on the local meteorological conditions at the time of the event. The results included in this report also do not consider the urban environment (e.g., shielding by or collapse of structures) which may affect the extent of prompt effects. It is important to note that any operational recommendations made using the estimates in this report are limited by the generic assumptions considered in the analysis and should not replace analyses made for a specific scenario/device. Furthermore, nuclear effects experts (John Hogan, SNL, and Byron Ristvet, Defense Threat Reduction Agency (DTRA)) have indicated that the accuracy of effects predictions below 0.5 kilotons (kT) or 500 tons nuclear yield have greater uncertainty because of the limited data available for the prompt effects in this regime. The Specialized Hazard Assessment Response Capability (SHARC) effects prediction tool was used for these analyses. Specifically, the NUKE model within SHARC 2021 Version 10.2 was used. NUKE models only the prompt effects following a nuclear detonation. The algorithms for predicting range-to-output data contained within the NUKE model are primarily based on nuclear test effects data. Probits have been derived from nuclear test data and the U.S. Environmental Protection Agency (EPA) protective action guides. Probits relate the probability of a hazard (e.g., fatality or injury) caused by a given insult (e.g., overpressure, thermal fluence, dose level). Several probits have been built into SHARC to determine the fatality and injury associated with a given level of insult. Some of these probits differ with varying yield. Such probits were used to develop the tables and plots in this report.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗
DOE OSTI2017

Light-curve Analysis of Ordinary Type IIP Supernovae Based on Neutrino-driven Explosion Simulations in Three Dimensions

Type II-plateau supernovae (SNe IIP) are the most numerous subclass of core-collapse SNe originating from massive stars. In the framework of the neutrino-driven explosion mechanism, we study the properties of the SN outburst for a red supergiant progenitor model and compare the corresponding light curves with observations of the ordinary Type IIP SN 1999em. Three-dimensional (3D) simulations of (parametrically triggered) neutrino-driven explosions are performed with the (explicit, finite-volume, Eulerian, multifluid hydrodynamics) code Prometheus, using a presupernova model of a 15 M {sub ⊙} star as initial data. On approaching homologous expansion, the hydrodynamic and composition variables of the 3D models are mapped to a spherically symmetric configuration, and the simulations are continued with the (implicit, Lagrangian, radiation hydrodynamics) code Crab to follow the evolution of the blast wave during the SN outburst. Our 3D neutrino-driven explosion model with an explosion energy of about 0.5×10{sup 51} erg produces {sup 56}Ni in rough agreement with the amount deduced from fitting the radioactively powered light-curve tail of SN 1999em. The considered presupernova model, 3D explosion simulations, and light-curve calculations can explain the basic observational features of SN 1999em, except for those connected to the presupernova structure of the outer stellar layers. Our 3D simulations show that the distribution of {sup 56}Ni-rich matter in velocity space is asymmetric with a strong dipole component that is consistent with the observations of SN 1999em. The monotonic decline in luminosity from the plateau to the radioactive tail in ordinary SNe IIP is a manifestation of the intense turbulent mixing at the He/H composition interface.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2011

Computer Simulation of Blast Waves in a Tunnel with Sudden Decrease in Cross Section

The case of an explosion in a tunnel where the blast wave encounters a sudden decrease in cross section is studied with quasi-one-dimensional (1D) and two-dimensional axisymmetric codes (2D) and the results are compared to experimental data. It is found that the numerical results from both codes are in good agreement until the interface at the change in cross section is encountered. Thereafter, however, the peak pressure derived with the codes is found to be significantly higher than the experimental results although the agreement between the 2D result and the experiment improves with increasing distance down the tunnel. Peak pressure and impulse per unit area obtained downstream of the interface with the 1D analysis are found to be substantially higher than with either the experiment or the 2D results. The reason for this is the time delay for the shock reflecting off the (vertical) rigid wall between the inner and outer tunnel radii to interact with the (supersonic) core flow into the decreased cross section. In the 1D case the reflected and transmitted shocks are formed instantaneously across the entire cross section resulting in higher pressure and increased shock speed downstream of the interface.

42 ENGINEERING↗
DOE OSTI2012

Rapid phylogenetic and functional classification of short genomic fragments with signature peptides

Background: Classification is difficult for shotgun metagenomics data from environments such as soils, where the diversity of sequences is high and where reference sequences from close relatives may not exist. Approaches based on sequence-similarity scores must deal with the confounding effects that inheritance and functional pressures exert on the relation between scores and phylogenetic distance, while approaches based on sequence alignment and tree-building are typically limited to a small fraction of gene families. We describe an approach based on finding one or more exact matches between a read and a precomputed set of peptide 10-mers. Results: At even the largest phylogenetic distances, thousands of 10-mer peptide exact matches can be found between pairs of bacterial genomes. Genes that share one or more peptide 10-mers typically have high reciprocal BLAST scores. Among a set of 403 representative bacterial genomes, some 20 million 10-mer peptides were found to be shared. We assign each of these peptides as a signature of a particular node in a phylogenetic reference tree based on the RNA polymerase genes. We classify the phylogeny of a genomic fragment (e.g., read) at the most specific node on the reference tree that is consistent with the phylogeny of observed signature peptides it contains. Using both synthetic data from four newly-sequenced soil-bacterium genomes and ten real soil metagenomics data sets, we demonstrate a sensitivity and specificity comparable to that of the MEGAN metagenomics analysis package using BLASTX against the NR database. Phylogenetic and functional similarity metrics applied to real metagenomics data indicates a signal-to-noise ratio of approximately 400 for distinguishing among environments. Our method assigns ~6.6 Gbp/hr on a single CPU, compared with 25 kbp/hr for methods based on BLASTX against the NR database. Conclusions: Classification by exact matching against a precomputed list of signature peptides provides comparable results to existing techniques for reads longer than about 300 bp and does not degrade severely with shorter reads. Orders of magnitude faster than existing methods, the approach is suitable now for inclusion in analysis pipelines and appears to be extensible in several different directions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

An Efficient Machine Learning Approach To Low-Complexity Filtering In Biological Sequences

Biological sequences contain low-complexity regions (LCRs) which produce superfluous matches in homology searches, and lead to slow execution of database search algorithms such as BLAST. These regions are efficiently identified by low-complexity filtering algorithms such as SDUST and SEG, which are included in the BLAST tool-suite. These algorithms target differing notions of complexity, so an algorithm which combines their sensitivities is pursued. A variety of features are derived from these algorithms, as well as a new filtering algorithm based on Lempel-Ziv complexity. Artificial sequences with known LCRs are used to train and evaluate an SVM classifier, which significantly outperforms the standalone filtering algorithms.

59 BASIC BIOLOGICAL SCIENCES↗