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DOE OSTI2025

Gaia: An AI-enabled genomic context–aware platform for protein sequence annotation

Protein sequence similarity search is fundamental to biology research, but current methods are typically not able to consider crucial genomic context information indicative of protein function, especially in microbial systems. Here, we present Gaia (Genomic AI Annotator), a sequence annotation platform that enables rapid, context-aware protein sequence search across genomic datasets. Gaia leverages gLM2, a mixed-modality genomic language model trained on both amino acid sequences and their genomic neighborhoods to generate embeddings that integrate sequence-structure-context information. This approach allows for the identification of functionally and/or evolutionarily related genes that are found in conserved genomic contexts, which may be missed by traditional sequence- or structure-based search alone. Gaia enables real-time search of a curated database comprising more than 85 million protein clusters from 131,744 microbial genomes. We compare the homolog retrieval performance of Gaia search against other embedding and alignment-based approaches. We provide Gaia as a web-based, freely available tool.

Jha, Nishant↗

DOE OSTI2025

Hybridization capture sequencing for Vibrio spp. and associated virulence factors

ABSTRACT Proliferation ofVibriospp. in aquatic ecosystems is associated with climate change and, concomitantly, increased incidence of vibriosis. They are autochthonous to aquatic environments globally, but traditional metagenomic methods for detecting and typing pathogenicVibriospp. are challenged by their presence in relatively low abundance and ability to persist in a viable but nonculturable state. In the study reported here, hybridization capture sequencing (HCS) was employed to profile low-abundanceVibriospp. in environmental samples. The HCS panel targeted a family of molecular chaperones (CPN60) specific to 69Vibriospp. and 162Vibrio-specific virulence factors. This approach was evaluated in parallel with traditional whole-community shotgun sequencing in a metagenomic analysis of water and oyster samples collected from the Chesapeake Bay. In addition,Vibrio parahaemolyticusandVibrio vulnificusstrains isolated from the samples were subjected to whole-genome sequencing to determine the genetic characteristics of pathogenicVibriospp. circulating in an aquatic environment. HCS, employed to determine the incidence and characterization of specificVibriospp., yielded significantly greater metagenomic insight, notably a variety of otherVibriospp., including detection ofVibrio cholerae,Vibrio fluvialis, andVibrio aestuarianus, in addition toVibrio parahaemolyticusandVibrio vulnificus, and also important virulence factors not detectable using traditional molecular methods. Thus, pathogenicVibriospp. in aquatic ecosystems may be far more common than currently understood. It is concluded that environmental surveillance should include HCS, a valuable tool for the detection and characterization of pathogenic agents in aquatic ecosystems, notably vibrios. IMPORTANCE The increasing prevalence of pathogenicVibriospp. in aquatic ecosystems, driven by climate change, is closely linked to a rise in cholera and vibriosis cases, emphasizing the need for improved environmental surveillance. Vibrios are naturally occurring in aquatic environments globally, but traditional metagenomic methods for detecting and typing pathogenicVibriospp. are challenged by their presence in relatively low abundance and ability to persist in a viable but nonculturable state. In the study reported here, hybridization capture sequencing was employed to profile low-abundanceVibriospp. in metagenomic samples, namely water and oysters collected from the Chesapeake Bay. This approach was evaluated in parallel with traditional whole-community shotgun sequencing and whole-genome sequencing ofVibrio parahaemolyticusandVibrio vulnificusstrains isolated from the samples. Results suggest pathogenicVibriospp. in aquatic ecosystems may be far more common than currently understood, when multiple methods are considered for environmental surveillance.

Microbiology↗

DOE OSTI2019

Evaluating the Effects of Missing Values and Mixed Data Types on Social Sequence Clustering Using t-SNE Visualization

© 2019 Association for Computing Machinery. The goal of this work is to investigate the impact of missing values in clustering joint categorical social sequences. Identifying patterns in sociodemographic longitudinal data is important in a number of social science settings. However, performing analytical operations, such as clustering on life course trajectories, is challenging due to the categorical and multidimensional nature of the data, their mixed data types, and corruption by missing and inconsistent values. Data quality issues were investigated previously on single variable sequences. To understand their effects on multivariate sequence analysis, we employ a dataset of mixed data types and missing values, a dissimilarity measure designed for joint categorical sequence data, together with dimensionality reduction methodologies in a systematic design of sequence clustering experiments. Given the categorical nature of our data, we employ an “edit” distance using optimal matching. Because each data record has multiple variables of different types, we investigate the impact of mixing these variables in a single dissimilarity measure. Between variables with binary values and those with multiple nominal values, we find that the ability to overcome missing data problems is more difficult in the nominal domain than in the binary domain. Additionally, alignment of leading missing values can result in systematic biases in dissimilarity matrices and subsequently introduce both artificial clusters and unrealistic interpretations of associated data domains. We demonstrate the usage of t-distributed stochastic neighborhood embedding to visually guide mitigation of such biases by tuning the missing value substitution cost parameter or determining an optimal sequence span.

Lazar, Alina↗

DOE OSTI2015

Pairwise Sequence Alignment Library

Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprint that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, a novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.

Jeff Daily, PNNL↗

DOE OSTI2021

Impact of short-read sequencing on the misassembly of a plant genome

Abstract Background Availability of plant genome sequences has led to significant advances. However, with few exceptions, the great majority of existing genome assemblies are derived from short read sequencing technologies with highly uneven read coverages indicative of sequencing and assembly issues that could significantly impact any downstream analysis of plant genomes. In tomato for example, 0.6% (5.1 Mb) and 9.7% (79.6 Mb) of short-read based assembly had significantly higher and lower coverage compared to background, respectively. Results To understand what the causes may be for such uneven coverage, we first established machine learning models capable of predicting genomic regions with variable coverages and found that high coverage regions tend to have higher simple sequence repeat and tandem gene densities compared to background regions. To determine if the high coverage regions were misassembled, we examined a recently available tomato long-read based assembly and found that 27.8% (1.41 Mb) of high coverage regions were potentially misassembled of duplicate sequences, compared to 1.4% in background regions. In addition, using a predictive model that can distinguish correctly and incorrectly assembled high coverage regions, we found that misassembled, high coverage regions tend to be flanked by simple sequence repeats, pseudogenes, and transposon elements. Conclusions Our study provides insights on the causes of variable coverage regions and a quantitative assessment of factors contributing to plant genome misassembly when using short reads and the generality of these causes and factors should be tested further in other species.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

Draft genome sequences of Bradyrhizobium shewense sp. nov. ERR11 T and Bradyrhizobium yuanmingense CCBAU 10071 T

The type strain of the prospective Bradyrhizobium shewense sp. nov. ERR11 T , was isolated from a nodule of the leguminous tree Erythrina brucei native to Ethiopia. The type strain Bradyrhizobium yuanmingense CCBAU 10071 T , was isolated from the nodules of Lespedeza cuneata in Beijing, China. The genomes of ERR11 T and CCBAU 10071 T were sequenced by DOE–JGI and deposited at the DOE–JGI genome portal as well as at the European Nucleotide Archive. The genome of ERR11 T is 9,163,226 bp in length and has 102 scaffolds, containing 8548 protein–coding and 86 RNA genes. The CCBAU 10071 T genome is arranged in 108 scaffolds and consists of 8,201,522 bp long and 7776 protein–coding and 85 RNA genes. Both genomes contain symbiotic genes, which are homologous to the genes found in the complete genome sequence of Bradyrhizobium diazoefficiens USDA110 T . The genes encoding for nodulation and nitrogen fixation in ERR11 T showed high sequence similarity with homologous genes found in the draft genome of peanut–nodulating Bradyrhizobium arachidis LMG 26795 T . The nodulation genes nolYA-nodD2D1YABCSUIJ-nolO-nodZ of ERR11 T and CCBAU 10071 T are organized in a similar way to the homologous genes identified in the genomes of USDA110 T , Bradyrhizobium ottawaense USDA 4 and Bradyrhizobium liaoningense CCBAU 05525. The genomes harbor hupSLCFHK and hypBFDE genes that code the expression of hydrogenase, an enzyme that helps rhizobia to uptake hydrogen released by the N 2 -fixation process and genes encoding denitrification functions napEDABC and norCBQD for nitrate and nitric oxide reduction, respectively. The genome of ERR11 T also contains nosRZDFYLX genes encoding nitrous oxide reductase. Based on multilocus sequence analysis of housekeeping genes, the novel species, which contains eight strains formed a unique group close to the B. ottawaense branch. Genome Average Nucleotide Identity (ANI) calculated between the genome sequences of ERR11 T and closely related sequences revealed that strains belonging to B. ottawaense branch (USDA4 and CCBAU15615), were the closest strains to the strain ERR11 T with 95.2% ANI. Type strain ERR11 T showed the highest DDH predicted value with CCBAU15615 (58.5%), followed by USDA 4 (53.1%). Nevertheless, the ANI and DDH values obtained between ERR11 T and CCBAU 15615 or USDA 4 were below the cutoff values (ANI ≥ 96.5%; DDH ≥ 70%) for strains belonging to the same species, suggesting that ERR11 T is a new species. Therefore, based on the phylogenetic analysis, ANI and DDH values, we formally propose the creation of B. shewense sp. nov. with strain ERR11 T (HAMBI 3532 T =LMG 30162 T ) as the type strain.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2015

Prediction of multi-drug resistance transporters using a novel sequence analysis method

There are many examples of groups of proteins that have similar function, but the determinants of functional specificity may be hidden by lack of sequencesimilarity, or by large groups of similar sequences with different functions. Transporters are one such protein group in that the general function, transport, can be easily inferred from the sequence, but the substrate specificity can be impossible to predict from sequence with current methods. In this paper we describe a linguistic-based approach to identify functional patterns from groups of unaligned protein sequences and its application to predict multi-drug resistance transporters (MDRs) from bacteria. We first show that our method can recreate known patterns from PROSITE for several motifs from unaligned sequences. We then show that the method, MDRpred, can predict MDRs with greater accuracy and positive predictive value than a collection of currently available family-based models from the Pfam database. Finally, we apply MDRpred to a large collection of protein sequences from an environmental microbiome study to make novel predictions about drug resistance in a potential environmental reservoir.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2014

Standardized Metadata for Human Pathogen/Vector Genomic Sequences

High throughput sequencing has accelerated the determination of genome sequences for thousands of human infectious disease pathogens and dozens of their vectors. The scale and scope of these data are enabling genotype-phenotype association studies to identify genetic determinants of pathogen virulence and drug/insecticide resistance, and phylogenetic studies to track the origin and spread of disease outbreaks. To maximize the utility of genomic sequences for these purposes, it is essential that metadata about the pathogen/vector isolate characteristics be collected and made available in organized, clear, and consistent formats. Here we report the development of the GSCID/BRC Project and Sample Application Standard, developed by representatives of the Genome Sequencing Centers for Infectious Diseases (GSCIDs), the Bioinformatics Resource Centers (BRCs) for Infectious Diseases, and the U.S. National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health (NIH), informed by interactions with numerous collaborating scientists. It includes mapping to terms from other data standards initiatives, including the Genomic Standards Consortium’s minimal information (MIxS) and NCBI’s BioSample/BioProjects checklists and the Ontology for Biomedical Investigations (OBI). The standard includes data fields about characteristics of the organism or environmental source of the specimen, spatial-temporal information about the specimen isolation event, phenotypic characteristics of the pathogen/vector isolated, and project leadership and support. By modeling metadata fields into an ontology-based semantic framework and reusing existing ontologies and minimum information checklists, the application standard can be extended to support additional project-specific data fields and integrated with other data represented with comparable standards. The use of this metadata standard by all ongoing and future GSCID sequencing projects will provide a consistent representation of these data in the BRC resources and other repositories that leverage these data, allowing investigators to identify relevant genomic sequences and perform comparative genomics analyses that are both statistically meaningful and biologically relevant.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2015

SNP Assay Development for Linkage Map Construction, Anchoring Whole-Genome Sequence, and Other Genetic and Genomic Applications in Common Bean

A total of 992,682 single-nucleotide polymorphisms (SNPs) was identified as ideal for Illumina Infinium II BeadChip design after sequencing a diverse set of 17 common bean (Phaseolus vulgaris L) varieties with the aid of next-generation sequencing technology. From these, two BeadChips each with >5000 SNPs were designed. The BARCBean6K_1 BeadChip was selected for the purpose of optimizing polymorphism among market classes and, when possible, SNPs were targeted to sequence scaffolds in the Phaseolus vulgaris 14× genome assembly with sequence lengths >10 kb. The BARCBean6K_2 BeadChip was designed with the objective of anchoring additional scaffolds and to facilitate orientation of large scaffolds. Analysis of 267 F2 plants from a cross of varieties Stampede × Red Hawk with the two BeadChips resulted in linkage maps with a total of 7040 markers including 7015 SNPs. With the linkage map, a total of 432.3 Mb of sequence from 2766 scaffolds was anchored to create the Phaseolus vulgaris v1.0 assembly, which accounted for approximately 89% of the 487 Mb of available sequence scaffolds of the Phaseolus vulgaris v0.9 assembly. A core set of 6000 SNPs (BARCBean6K_3 BeadChip) with high genotyping quality and polymorphism was selected based on the genotyping of 365 dry bean and 134 snap bean accessions with the BARCBean6K_1 and BARCBean6K_2 BeadChips. The BARCBean6K_3 BeadChip is a useful tool for genetics and genomics research and it is widely used by breeders and geneticists in the United States and abroad.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Machine-Learning-Based High-Resolution Earthquake Catalog Reveals How Complex Fault Structures Were Activated during the 2016–2017 Central Italy Sequence

The 2016–2017 central Italy seismic sequence occurred on an 80 km long normal-fault system. The sequence initiated with the Mw 6.0 Amatrice event on 24 August 2016, followed by the Mw 5.9 Visso event on 26 October and the Mw 6.5 Norcia event on 30 October. We analyze continuous data from a dense network of 139 seismic stations to build a high-precision catalog of ~900,000 earthquakes spanning a 1 yr period, based on arrival times derived using a deep-neural-network-based picker. Our catalog contains an order of magnitude more events than the catalog routinely produced by the local earthquake monitoring agency. Aftershock activity reveals the geometry of complex fault structures activated during the earthquake sequence and provides additional insights into the potential factors controlling the development of the largest events. Activated fault structures in the northern and southern regions appear complementary to faults activated during the 1997 Colfiorito and 2009 L’Aquila sequences, suggesting that earthquake triggering primarily occurs on critically stressed faults. Delineated major fault zones are relatively thick compared to estimated earthquake location uncertainties, and a large number of kilometer-long faults and diffuse seismicity were activated during the sequence. These properties might be related to fault age, roughness, and the complexity of inherited structures. The rich details resolvable in this catalog will facilitate continued investigation of this energetic and well-recorded earthquake sequence.

58 GEOSCIENCES↗

DOE OSTI2023

Field Demonstration of the Brick Ontology to Scale up the Deployment of ASHRAE Guideline 36 Control Sequences

Many commercial buildings have a vast network of sensors as part of their building automation systems (BAS) that allows opportunities for energy consumption and cost savings by deploying advanced control sequences. However, this resource is often underutilized since BAS are typically programmed with simple control sequences with limited potential to deliver on these opportunities. The recent availability of ASHRAE Guideline 36 (G36) with advanced HVAC control sequences supports control retrofits in existing buildings to unlock much of the savings potential. However, barriers such as the lack of standard naming convention of building assets and data points, proprietary equipment and BAS, and the inherent uniqueness of buildings and their systems prevent building stakeholders from adopting any “plug-and-play” implementation of G36. Instead, control vendors must often undertake the manual and labor-intensive point mapping process to identify a data stream’s functional and spatial relationship within the HVAC system along with other relevant contexts and map it to the new control sequences. The vendor must carry out the point mapping process in each individual building since the mapping is unlikely to port over to another building. Even for the same building, the point mapping process can occur multiple times if various control vendors implement different control retrofits and/or multiple control retrofits happen over the lifecycle of the building. Then, there is the likelihood that G36 control sequences are programmed uniquely to the building, preventing the same implementation from being reused in another. Therefore, this paper presents a field demonstration of how we leveraged the Brick ontology with BACnet, OpenBuildingControl’s Control Description Language (CDL), and open-source support tools to implement scalable and portable advanced building controls. These tools provide standardized semantic descriptions and relationships of the building’s assets and data points (Brick), standardized communication protocol to read from and write to the building’s BAS (BACnet), and standardized code implementations (CDL) of standardized advanced control strategies (G36). We implemented G36’s hot water supply temperature setpoint reset in a Berkeley, CA building for this field demonstration. This field demonstration aims to show how integrating these tools may streamline the deployment of advanced control sequences such as G36 in a consistent manner regardless of differences found across buildings.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2015

HIV Sequence Compendium 2015

This compendium is an annual printed summary of the data contained in the HIV sequence database. We try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2015. Hence, though it is published in 2015 and called the 2015 Compendium, its contents correspond to the 2014 curated alignments on our website. The number of sequences in the HIV database is still increasing. In total, at the end of 2014, there were 624,121 sequences in the HIV Sequence Database, an increase of 7% since the previous year. This is the first year that the number of new sequences added to the database has decreased compared to the previous year. The number of near complete genomes (>7000 nucleotides) increased to 5834 by end of 2014. However, as in previous years, the compendium alignments contain only a fraction of these. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/ content/sequence/NEWALIGN/align.html As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

The MAVRIC-Shift Sequence in SCALE for Radiation Transport and Shielding Calculations with Automated Variance Reduction and Parallel Computing

A new MAVRIC-Shift sequence has been implemented and tested within the SCALE Code System to provide parallel computing capabilities for radiation transport and shielding analysis with automated variance reduction. This new sequence provides the most widely used capabilities of the MAVRIC sequence and also features the highly scalable Shift Monte Carlo solver, thus enabling faster time-to-solution when run on multiple cores. This report provides a summary of the theory of variance reduction approaches in MAVRIC and the integration of Shift into the MAVRIC sequence of SCALE. Similarities and differences in methodologies between the traditional MAVRIC sequence and the new MAVRIC-Shift sequence are discussed. Validation cases are presented with models of radiation shielding experiments and verification is provided with a series of practical application cases of interest to the US Nuclear Regulatory Commission, the sponsors of this work, including spent nuclear fuel transportation and storage systems.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2022

Focusing Ions at Atmospheric Pressure using Nonlinear DC Voltage Sequences Applied to a Stacked Ring Ion Guide

Many modern ion mobility (IM) and mass spectrometers (MS) operate under low pressure (= 10 Torr) and employ high voltage radiofrequencies (RF) to provide ion confinement. Unfortunately, RF effectiveness drastically decreases as pressure increases, and few techniques for focusing ions at elevated pressures exist. Here we demonstrate a new approach for focusing ions at atmospheric pressure (AP) by applying nonlinear DC voltage sequences following quadratic and power (exponential) functions to a stacked ring ion guide. We used ion trajectory simulations to rigorously explore how ions react to nonlinear electric fields and validate the simulations with a set of ion current measurements performed at AP. Ion trajectory simulations show that ions initially defocus near the entrance of the device but then become intensely focused as they travel through the device. Contour plots for both nonlinear voltage sequences show electric field lines that increasingly curve inwards as a function of distance, resulting in spatial ion focusing. Experimental ion current and spot size measurements were performed at AP using a 10-cm stacked ring ion guide and a segmented Faraday cup detector. Quadratic sequences produced ~5% smaller spot sizes (~22.8 mm) and ~25% higher ion current compared to a linear voltage sequence (~24.0 mm). Alternatively, power sequences produced ~64% smaller spot sizes (~8.7 mm), albeit with ~10x lower ion current. However, both nonlinear voltage sequences produced similar ion currents at the center of the Faraday cup detector, indicating that higher ion densities are achieved when using nonlinear voltage gradients. These results demonstrate a new way to focus ions at AP, and the capabilities demonstrated here provide fundamental insights on how to keep ions inside analytical devices at elevated pressures without RF.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

UAE6 - Wind Tunnel Tests Data - UAE6 - Sequence B - Raw Data

Sequences B, C, and D: Downwind Baseline (F), Downwind Low Pitch (F), Downwind High Pitch (F) This test sequence used a downwind, teetered turbine with a 3.4° cone angle. The wind speed ranged from 5 m/s to 25 m/s. Yaw angles of ±180° were achieved at low wind speeds, and yaw angles of -20° to 10° were achieved for high wind speeds. The blade tip pitch was 3° for sequence B, 0° for sequence C, and 6° for sequence D. These three sequences were interleaved during testing because the pitch angle change was easily made by the turbine operator. The rotor rotated at 72 RPM. Blade and probe pressure measurements were collected.

17 WIND ENERGY↗

DOE OSTI2022

UAE6 - Wind Tunnel Tests Data - UAE6 - Sequence C - Raw Data

17 WIND ENERGY↗

DOE OSTI2022

UAE6 - Wind Tunnel Tests Data - UAE6 - Sequence D - Raw Data

17 WIND ENERGY↗

DOE OSTI2022

UAE6 - Wind Tunnel Tests Data - UAE6 - Sequence 8 - Raw Data

Sequences 8 and 9: Downwind Sonics (F,P) and Downwind Sonics Parked (P) This test sequence used an upwind, rigid turbine with a 0° cone angle. The wind speed ranged from 5 m/s to 25 m/s. Yaw angles of 0° to 60° were achieved. The blade tip pitch was 3°. The rotor rotated at 72 RPM during Sequence 8, but it was parked during Sequence 9. Blade pressure measurements were collected. The five-hole probes were removed and the plugs were installed. Plastic tape 0.03-mm-thick was used to smooth the interface between the plugs and the blade. The teeter dampers were replaced with rigid links, and these two channels were flagged as not applicable by setting the measured values in the data file to –99999.99 Nm. The teeter link load cell was pre-tensioned to 40,000 N. During post-processing, the probe channels were set to read -99999.99. Sonic anemometers were mounted on a strut downwind of the turbine. The strut was mounted to the T-frame, which was rotated to align the anemometers aft of the 9% and 49% radius locations at hub height. Because of this configuration, the tunnel balance data are considered invalid. Sequence 9 was designed to compare the downwind sonic anemometer readings with the upwind sonic anemometers without interference from the turbine. The rotor was parked with the instrumented blade at 0° azimuth. All pressure measurements obtained in Sequence 9 are invalid because sufficient time for temperature stabilization did not occur, thus all associated data values were flagged as not applicable by setting the measured values in the data file to 0.0000 Pa. This test is further described in Appendix G.

17 WIND ENERGY↗