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At least 343 records · Page 19

All sources NASA NTRS DOE OSTI

DOE OSTI2020

Genome‐wide association study of multiple yield traits in a diversity panel of polyploid sugarcane ( Saccharum spp.)

Abstract Sugarcane ( Saccharum spp.) is an important economic crop, contributing up to 80% of sugar and approximately 60% of biofuel globally. To meet the increased demand for sugar and biofuel supplies, it is critical to breed sugarcane cultivars with robust performance in yield traits. Therefore, dissection of causal DNA sequence variants is of great importance, as it provides genetic resources and fundamental information for crop improvement. In this study, we analyzed nine yield traits in a sugarcane diversity panel consisting of 308 accessions primarily selected from the World Collection of Sugarcane and Related Grasses. By genotyping the diversity panel via target enrichment sequencing, we identified a large number of sequence variants. Genome‐wide association studies between the markers and traits were conducted, taking dosages and gene actions into consideration. In total, 217 nonredundant markers and 225 candidate genes were identified to be significantly associated with the yield traits, which can serve as a comprehensive genetic resource database for future gene identification, characterization, and selection for sugarcane improvement. We further investigated runs of homozygosity (ROH) in the sugarcane diversity panel. We characterized 282 ROHs and found that the occurrence of ROHs in the genome were nonrandom and probably under selection. The ROHs were associated with total weight and dry weight, and high ROHs resulted in a decrease in the two traits. This study suggests that genomic inbreeding has led to negative impacts on sugarcane yield.

Yang, Xiping↗

DOE OSTI2021

Metagenomic Insights Into the Microbial Iron Cycle of Subseafloor Habitats

Microbial iron cycling influences the flux of major nutrients in the environment (e.g., through the adsorptive capacity of iron oxides) and includes biotically induced iron oxidation and reduction processes. The ecological extent of microbial iron cycling is not well understood, even with increased sequencing efforts, in part due to limitations in gene annotation pipelines and limitations in experimental studies linking phenotype to genotype. This is particularly true for the marine subseafloor, which remains undersampled, but represents the largest contiguous habitat on Earth. To address this limitation, we used FeGenie, a database and bioinformatics tool that identifies microbial iron cycling genes and enables the development of testable hypotheses on the biogeochemical cycling of iron. Herein, we survey the microbial iron cycle in diverse subseafloor habitats, including sediment-buried crustal aquifers, as well as surficial and deep sediments. We inferred the genetic potential for iron redox cycling in 32 of the 46 metagenomes included in our analysis, demonstrating the prevalence of these activities across underexplored subseafloor ecosystems. We show that while some processes (e.g., iron uptake and storage, siderophore transport potential, and iron gene regulation) are near-universal, others (e.g., iron reduction/oxidation, siderophore synthesis, and magnetosome formation) are dependent on local redox and nutrient status. Additionally, we detected niche-specific differences in strategies used for dissimilatory iron reduction, suggesting that geochemical constraints likely play an important role in dictating the dominant mechanisms for iron cycling. Overall, our survey advances the known distribution, magnitude, and potential ecological impact of microbe-mediated iron cycling and utilization in sub-benthic ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2012

Comparison of Statistical Estimation Techniques for Mars Entry, Descent, and Landing Reconstruction from MEDLI-like Data Sources

Flight data from an entry, descent, and landing (EDL) sequence can be used to reconstruct the vehicle's trajectory, aerodynamic coefficients and the atmospheric profile experienced by the vehicle. Past Mars missions have contained instruments that do not provide direct measurement of the freestream atmospheric conditions. Thus, the uncertainties in the atmospheric reconstruction and the aerodynamic database knowledge could not be separated. The upcoming Mars Science Laboratory (MSL) will take measurements of the pressure distribution on the aeroshell forebody during entry and will allow freestream atmospheric conditions to be partially observable. This data provides a mean to separate atmospheric and aerodynamic uncertainties and is part of the MSL EDL Instrumentation (MEDLI) project. Methods to estimate the flight performance statistically using on-board measurements are demonstrated here through the use of simulated Mars data. Different statistical estimators are used to demonstrate which estimator best quantifies the uncertainties in the flight parameters. The techniques demonstrated herein are planned for application to the MSL flight dataset after the spacecraft lands on Mars in August 2012.

Dutta, Soumyo↗

NASA NTRS2003

Fidelity and enhanced sensitivity of differential transcription profiles following linear amplification of nanogram amounts of endothelial mRNA

Although mRNA amplification is necessary for microarray analyses from limited amounts of cells and tissues, the accuracy of transcription profiles following amplification has not been well characterized. We tested the fidelity of differential gene expression following linear amplification by T7-mediated transcription in a well-established in vitro model of cytokine [tumor necrosis factor alpha (TNFalpha)]-stimulated human endothelial cells using filter arrays of 13,824 human cDNAs. Transcriptional profiles generated from amplified antisense RNA (aRNA) (from 100 ng total RNA, approximately 1 ng mRNA) were compared with profiles generated from unamplified RNA originating from the same homogeneous pool. Amplification accurately identified TNFalpha-induced differential expression in 94% of the genes detected using unamplified samples. Furthermore, an additional 1,150 genes were identified as putatively differentially expressed using amplified RNA which remained undetected using unamplified RNA. Of genes sampled from this set, 67% were validated by quantitative real-time PCR as truly differentially expressed. Thus, in addition to demonstrating fidelity in gene expression relative to unamplified samples, linear amplification results in improved sensitivity of detection and enhances the discovery potential of high-throughput screening by microarrays.

Evaluation Studies↗

NASA NTRS1988

Cool circumstellar matter around nearby main-sequence stars

Stars are presented which have characteristics similar to Vega and other main-sequence stars with cool dust disks, based on the IRAS Point Source Catalog fluxes. The objects are selected to have a 60-micron/100-micron ratio similar to Vega, Beta Pic, Alpha PsA, and Epsilon Eri, and they are also required to show evidence of extension in the IRAS Working Survey Database. The fluxes are modeled using a blackbody energy distribution. The temperatures derived range from 50 to 650 K. The diameters of the dust disks observed by IRAS are estimated.

Walker, H. J.↗

DOE OSTI2021

NASA GeneLab RNA-seq consensus pipeline: Standardized processing of short-read RNA-seq data

With the development of transcriptomic technologies, we are able to quantify precise changes in gene expression profiles from astronauts and other organisms exposed to spaceflight. Members of NASA GeneLab and GeneLab-associated analysis working groups (AWGs) have developed a consensus pipeline for analyzing short-read RNA-sequencing data from spaceflight-associated experiments. The pipeline includes quality control, read trimming, mapping, and gene quantification steps, culminating in the detection of differentially expressed genes. This data analysis pipeline and the results of its execution using data submitted to GeneLab are now all publicly available through the GeneLab database. We present here the full details and rationale for the construction of this pipeline in order to promote transparency, reproducibility, and reusability of pipeline data; to provide a template for data processing of future spaceflight-relevant datasets; and to encourage cross-analysis of data from other databases with the data available in GeneLab.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2000

Landscape Evolution, A Comparison of Form and Process

This project's goals were to collect, analyze and interpret 3-dimensional physiographic data for understanding the processes responsible for landscape modification. The primary landforms to be studied were Neogene cinder cones in Arizona (San Francisco Volcanic Field (SFVF), Coconino and Kaibab National Forests, Arizona). We also obtained and are still analyzing digital topographic data for the Long Valley-White Mountains area of California, which display Quaternary normal fault scarps, as well as extensive evidence of degradation. The work resulted in a large database of measured rates of downslope transport of slope debris. It was hypothesized that the work would increase our understanding of process-response models of hillslope degradation, and of the effects of climate change and other parameters on degradation rates. In greater detail, our primary goal was to compare evolutionary sequences of hillslopes, as exemplified by the topography of landforms of the same type but of different ages, with measurements of the surficial processes active on the landforms. Assuming that other parameters, such as hillslope materials and vegetation are held constant, and that the effects of changing climate are negligible, then the sediment transport rates measured today on the landforms should be the same as those calculated from the inversion of landform topography by use of a diffusion-type model. However, if the effects of changing climate or other factors are not negligible, then the observed transport rates would differ from those which must be invoked to explain the current topography. We hypothesized in fact that because degradation on the event scale is highly transient and localized, we would find a wide divergence between modern, measured transport rates, and rates calculated by global landform inversion or modeling. Because of the length of time involved in collection of sufficient data on current degradation rates, we are still continuing to analyse and interpret the data. Completion of the work will increase our understanding of the potential effects of anthropogenic climate and surficial change on the Earth's solid surface, and possibly allow us to constrain paths of hill-slope evolution following anthropogenic modifications, as well as compare the short-term with the long-term rates of hillslope degradation.

Bursik, Marcus I.↗

NASA NTRS1995

Nocturnal Observations of the Semidiurnal Tide at a Midlatitude Site

Fabry-Perot interferometer observations of the mesospheric hydroxyl emission and the lower thermospheric OI (5577A) emission have been conducted from an airglow observatory at a dark field site in southeastern Michigan for the past several years. The primary functions of the observatory are to provide a database for correlative observations with the UARS satellite and to provide a synoptic measurement program for the coupling energetics and dynamics of atmospheric regions effort, An intensive operational effort between May 1993 and July 1994 has resulted in a substantial data set from which neutral winds have been determined from the bifilter acquisition sequence. A 'best fit' analysis in the least squares sense of the simultaneous measurements of the neutral winds to a 12-hour periodicity has provided amplitude and phase parameters for the semidiurnal tide as well as a measure of the mean wind. The measured tidal amplitude is greater at the higher altitude, though the seasonal behavior at both altitudes is similar with greater amplitudes during August/September and April/May. Both meridional and zonal wind components are consistent with a semidiurnal tidal description during the entire observational sequence except for the May to July 1993 period. The mean winds show annual variation in the meridional flow, being equatorward from May to October and poleward during the winter. The zonal flow is primarily eastward during the entire observational window with higher speed flows during May/June at the higher attitude and June/July at the lower altitude. A comparison with a semidiurnal tidal model indicates that the measured tidal amplitudes are a factor of 2 times greater, while the phases show similar equinoctial transitions.

Niciejewski, R. J.↗

DOE OSTI2022

Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity

Despite advances in sequencing, lack of standardization makes comparisons across studies challenging and hampers insights into the structure and function of microbial communities across multiple habitats on a planetary scale. Here we present a multi-omics analysis of a diverse set of 880 microbial community samples collected for the Earth Microbiome Project. We include amplicon (16S, 18S, ITS) and shotgun metagenomic sequence data, and untargeted metabolomics data (liquid chromatography-tandem mass spectrometry and gas chromatography mass spectrometry). We used standardized protocols and analytical methods to characterize microbial communities, focusing on relationships and co-occurrences of microbially related metabolites and microbial taxa across environments, thus allowing us to explore diversity at extraordinary scale. In addition to a reference database for metagenomic and metabolomic data, we provide a framework for incorporating additional studies, enabling the expansion of existing knowledge in the form of an evolving community resource. We demonstrate the utility of this database by testing the hypothesis that every microbe and metabolite is everywhere but the environment selects. Our results show that metabolite diversity exhibits turnover and nestedness related to both microbial communities and the environment, whereas the relative abundances of microbially related metabolites vary and co-occur with specific microbial consortia in a habitat-specific manner. We additionally show the power of certain chemistry, in particular terpenoids, in distinguishing Earth’s environments (for example, terrestrial plant surfaces and soils, freshwater and marine animal stool), as well as that of certain microbes including Conexibacter woesei (terrestrial soils), Haloquadratum walsbyi (marine deposits) and Pantoea dispersa (terrestrial plant detritus). This Resource provides insight into the taxa and metabolites within microbial communities from diverse habitats across Earth, informing both microbial and chemical ecology, and provides a foundation and methods for multi-omics microbiome studies of hosts and the environment.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

COMPILE: a GWAS computational pipeline for gene discovery in complex genomes

Abstract Background Genome-Wide Association Studies (GWAS) are used to identify genes and alleles that contribute to quantitative traits in large and genetically diverse populations. However, traits with complex genetic architectures create an enormous computational load for discovery of candidate genes with acceptable statistical certainty. We developed a streamlined computational pipeline for GWAS (COMPILE) to accelerate identification and annotation of candidate maize genes associated with a quantitative trait, and then matches maize genes to their closest rice and Arabidopsis homologs by sequence similarity. Results COMPILE executed GWAS using a Mixed Linear Model that incorporated, without compression, recent advancements in population structure control, then linked significant Quantitative Trait Loci (QTL) to candidate genes and RNA regulatory elements contained in any genome. COMPILE was validated using published data to identify QTL associated with the traits of α-tocopherol biosynthesis and flowering time, and identified published candidate genes as well as additional genes and non-coding RNAs. We then applied COMPILE to 274 genotypes of the maize Goodman Association Panel to identify candidate loci contributing to resistance of maize stems to penetration by larvae of the European Corn Borer ( Ostrinia nubilalis ). Candidate genes included those that encode a gene of unknown function, WRKY and MYB-like transcriptional factors, receptor-kinase signaling, riboflavin synthesis, nucleotide-sugar interconversion, and prolyl hydroxylation. Expression of the gene of unknown function has been associated with pathogen stress in maize and in rice homologs closest in sequence identity. Conclusions The relative speed of data analysis using COMPILE allowed comparison of population size and compression. Limitations in population size and diversity are major constraints for a trait and are not overcome by increasing marker density. COMPILE is customizable and is readily adaptable for application to species with robust genomic and proteome databases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1986

Recent progress in Precambrian paleobiology

Ongoing studies at UCLA include the following: (1) investigations in Archean and Proterozoic sequences of various locations; (2) laboratory and field studies of modern microbial biocoenoses (analogues of Precambrian microbial communities) especially those at Laguna Mormona, Baja California, Mexico; (3) development of new laboratory techniques for the separation and concentration of minute cellularly preserved fossils for isotopic and organic geochemical analyses; and (4) assembly of a computerized database for assessment of the timing and nature of major events occurring during Precambrian biotic evolution, and of the potential applicability of ancient microbiotas to problems of global biostratigraphy and biogeography.

Schopf, J. W.↗

NASA NTRSDate not supplied

NASA GeneLab: Open Science for Life in Space

The NASA GeneLab project capitalizes on multi-omic technologies to maximize the return on spaceflight experiments. To do this, GeneLab maintains a publicly accessible database (GLDS) that houses spaceflight and spaceflight relevant multi-omics data and collaborates with NASA principal investigators and projects to generate additional omics data. GeneLab houses more than 350 transcriptomic, proteomic, metabolomic and epigenomic datasets from plant, animal and microbial experiments, with a growing number of these having been produced by the GeneLab Sequencing Lab. The GLDS contains rich metadata about each experiment and has integrated radiation dosimetry data from experiments flown on the Space Shuttle, International Space Station, and Free Flying spacecrafts. With the increasing amount and complexity of omics data being generated, GeneLab utilizes community-defined, common models for metadata and terminology so that omics data and results are discoverable and reliably reproducible. GeneLab uses the ISA-Tab specification and semantic model for organizing and representing omics metadata. In addition to metadata standards, data files must be open-source file or common exchange formats to ensure accessibility and usability by all users. To ease data ingestion and transfer, the web-based submission tool allows PIs a user-friendly user interface to curate, organize, and publish their space relevant omics data. In the more recent years, data curation and submission portal has incorporated the FAIR principles making data findable, accessible, interoperable, and reusable. To increase reusability of data, GeneLab has implemented an effort to present processed data in the GLDS in addition to the raw omics data. The processed data will enable interpretation of the data by a larger group of students, scientists and the general public. Standard pipelines for the transformation of raw data into visualizations were developed by four GeneLab Analysis Working Groups (animals, plants, microbes, multi-omics) comprised of over 200 scientists from NASA, industry, and academia. To explore the data, the GLDS provides users various tools for data analysis, collaborative workspace for file storage and sharing, and a visualization portal. The analysis platform built using the Galaxy toolshed provides access to a broad variety of users including those with limited bioinformatics experience and students to learn how to analyze spaceflight omics data. The visualization portal takes GeneLab one step closer to data democratization by removing all bioinformatics requisites to interpret transcriptomics data hosted in the repository. To train the next generation of scientists, NASA offers training programs such as GeneLab 4 High School (GL4HS) and GeneLab 4 Universities. NLM Curation at a Scale Workshop 2022 | NASA GeneLab (GL4U) to teach students bioinformatics and computational biology methods to analyze omics data. Discoveries made using GeneLab have begun and will continue to deepen our understanding of biology, advance the field of genomics, and help to discover cures for diseases, create better diagnostic tools, and ultimately allow astronauts to better withstand the rigors of long-duration spaceflight.

GeneLab↗

DOE OSTI2022

The Preprocessing of Galaxies in the Early Stages of Cluster Formation in Abell 1882 at z = 0.139

A rare opportunity to distinguish between internal and environmental effects on galaxy evolution is afforded by "SuperGroups," systems that are rich and massive, but include several comparably rich substructures, surrounded by filaments. We present here a multiwavelength photometric and spectroscopic study of the galaxy population in the SuperGroup Abell 1882 (A1882) at z = 0.139, combining new data from the MMT and Hectospec with archival results from the Galaxy And Mass Assembly survey, the Sloan Digital Sky Survey, the Nasa/IPAC Extragalactic Database, the Gemini Multi-Object Spectrograph, and the Galaxy Evolution Explorer. These provide spectroscopic classifications for 526 member galaxies, across wide ranges of local density and velocity dispersion. We identify three prominent filaments along which galaxies seem to be entering the SuperGroup (mostly in E–W directions). A1882 has a well-populated red sequence, containing most galaxies with stellar mass >10 10.5 M Sun , and a pronounced color–density relation even within its substructures. Thus, galaxy evolution responds to the external environment as strongly in these unrelaxed systems as we find in rich and relaxed clusters. From these data, local density remains the primary factor, with a secondary role for distance from the inferred center of the entire structure's potential well. The effects on star formation, as traced by optical and near-UV colors, depend on galaxy mass. We see changes in lower-mass galaxies (M < 10 10.5 M Sun ) at four times the virial radius of major substructures, while the more massive near-UV Green Valley galaxies show low levels of star formation within two virial radii. The suppression of star formation ("quenching") occurs in the infall regions of these structures even before the galaxies enter the denser group environment.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

DIVA/DeviceEditor (DIVA) v6.0.0

The DIVA software interfaces a process in which researchers design their DNA with a web-based graphical user interface (DeviceEditor), submit their designs to a central queue, and a few weeks later receive their sequence-verified clonal constructs. Each researcher independently designs the DNA to be constructed with a web-based BioCAD tool, and presses a button to submit their designs to a central queue. Researchers have web-based access to their DNA design queues, and can track the progress of their submitted designs as they progress from "evaluation", to "waiting for reagents", to "in progress", to "complete". Researchers access their completed constructs through the central DNA repository. Along the way, all DNA construction success/failure rates are captured in a central database. Once a design has been submitted to the queue, a small number of dedicated staff evaluate the design for feasibility and provide feedback to the responsible researcher if the design is either unreasonable (e.g., encompasses a combinatorial library of a billion constructs) or small design changes could significantly facilitate the downstream implementation process. The dedicated staff then use DNA assembly design automation software to optimize the DNA construction process for the design, leveraging existing parts from the DNA repository where possible and ordering synthetic DNA where necessary. Once all requisite process inputs are available, the design progresses from "waiting for reagents" to "in progress" in the design queue. Human-readable and machine-parseable DNA construction protocols output by the DNA assembly design automation software are then executed by the dedicated staff exploiting lab automation devices wherever possible. Since the all employed DNA construction methods are sequence-agnostic, standardized (utilize the same enzymatic master mixes and reaction conditions), completely independent DNA construction tasks can be aggregated into the same multi-well plates and pursued in parallel. The resulting sets of cloned constructs can then be screened by high-throughput next-gen sequencing platforms for sequence correctness. A combination of long read-length (e.g., PacBio) and paired-end read platforms (e.g., Illumina) would be exploited depending the particular task at hand (e.g., PacBio might be sufficient to screen a set of pooled constructs with significant gene divergence). Post sequence verification, designs for which at least one correct clone was identified will progress to a "complete" status, while designs for which no correct clones were identified will progress to a "failure" status. Depending on the failure mode (e.g., no transformants), and how many prior attempts/variations of assembly protocol have been already made for a given design, subsequent attempts may be made or the design can progress to a "permanent failure" state. All success and failure rate information will be captured during the process, including at which stage a given clonal construction procedure failed (e.g., no PCR product) and what the exact failure was (e.g. assembly piece 2 missing). This success/failure rate data can be leveraged to refine the DNA assembly design process.

Plahar, Hector↗

DOE OSTI2022

White Dwarf Binaries across the H-R Diagram

We created the APOGEE-GALEX-Gaia catalog to study white dwarf (WD) binaries. This database aims to create a minimally biased sample of WD binary systems identified from a combination of GALEX, Gaia, and APOGEE data to increase the number of WD binaries with orbital parameters and chemical compositions. We identify 3414 sources as WD binary candidates, with nondegenerate companions of spectral types between F and M, including main-sequence stars, main-sequence binaries, subgiants, sub-subgiants, red giants, and red clump stars. Among our findings are (a) a total of 1806 systems having inferred WD radii R < 25 R ⊕ , which constitute a more reliable group of WD binary candidates within the main sample; (b) a difference in the metallicity distribution function between WD binary candidates and the control sample of most luminous giants (M H < -3.0); (c) the existence of a population of sub-subgiants with WD companions; (d) evidence for shorter periods in binaries that contain WDs compared to those that do not, as shown by the cumulative distributions of APOGEE radial velocity shifts; (e) evidence for systemic orbital evolution in a sample of 252 WD binaries with orbital periods, based on differences in the period distribution between systems with red clump, main-sequence binary, and sub-subgiant companions and systems with main-sequence or red giant companions; and (f) evidence for chemical enrichment during common envelope (CE) evolution, shown by lower metallicities in wide WD binary candidates (P > 100 days) compared to post-CE (P < 100 days) WD binary candidates.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

Interactive tools for functional annotation of bacterial genomes

Automated annotations of protein functions are error-prone because of our lack of knowledge of protein functions. For example, it is often impossible to predict the correct substrate for an enzyme or a transporter. Furthermore, much of the knowledge that we do have about the functions of proteins is missing from the underlying databases. We discuss how to use interactive tools to quickly find different kinds of information relevant to a protein’s function. Many of these tools are available via PaperBLAST (http://papers.genomics.lbl.gov). Combining these tools often allows us to infer a protein’s function. Ideally, accurate annotations would allow us to predict a bacterium’s capabilities from its genome sequence, but in practice, this remains challenging. We describe interactive tools that infer potential capabilities from a genome sequence or that search a genome to find proteins that might perform a specific function of interest.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2007

Web-Based Environment for Maintaining Legacy Software

Advanced Tool Integration Environment (ATIE) is the name of both a software system and a Web-based environment created by the system for maintaining an archive of legacy software and expertise involved in developing the legacy software. ATIE can also be used in modifying legacy software and developing new software. The information that can be encapsulated in ATIE includes experts documentation, input and output data of tests cases, source code, and compilation scripts. All of this information is available within a common environment and retained in a database for ease of access and recovery by use of powerful search engines. ATIE also accommodates the embedment of supporting software that users require for their work, and even enables access to supporting commercial-off-the-shelf (COTS) software within the flow of the experts work. The flow of work can be captured by saving the sequence of computer programs that the expert uses. A user gains access to ATIE via a Web browser. A modern Web-based graphical user interface promotes efficiency in the retrieval, execution, and modification of legacy code. Thus, ATIE saves time and money in the support of new and pre-existing programs.

Tigges, Michael↗

DOE OSTI2026

nf-core/proteinfamilies: a scalable pipeline for the generation of protein families

The growth of metagenomics-derived amino acid sequence data has transformed our understanding of protein function, microbial diversity, and evolutionary relationships. However, the vast majority of these proteins remain functionally uncharacterized. Grouping the millions of such uncharacterized sequences with the few experimentally characterized ones allows the transfer of annotations, while the inspection of conserved residues with multiple sequence alignments can provide clues to function, even in the absence of existing functional information. To address the challenges associated with this data surge and the need to group sequences, we present a scalable, open-source, parametrizable Nextflow pipeline (nf-core/proteinfamilies) that generates nascent protein families or assigns new proteins to existing families. The computational benchmarks demonstrated that resource usage scales approximately linearly with input size, and the biological benchmarks showed that the generated protein families closely resemble manually curated families in widely used databases.

Nextflow↗