An official website of the United States government
Aligning to a linear reference genome can result in a higher percentage of reads going unmapped or being incorrectly mapped owing to variations not captured by the reference, otherwise known as reference bias. Recently, in efforts to mitigate reference bias, there has been a movement to switch to using pangenomes, a collection of genomes, as the reference. In this paper, we introduce Moni-align, the first short-read pangenome aligner built on the r-index, a variation of the classical FM-index that can index collections of genomes in O(r)-space, whereris the number of runs in the Burrows–Wheeler transform. Moni-align uses a seed-and-extend strategy for aligning reads, utilizing maximal exact matches as seeds, which can be efficiently obtained with ther-index. Using both simulated and real short-read data sets, we demonstrate that Moni-align achieves alignment accuracy comparable to vg map and vg giraffe, the leading pangenome aligners. Although currently best suited for aligning to localized pangenomes owing to computational constraints, Moni-align offers a robust foundation for future optimizations that could further broaden its applicability.
more »
« less
Burch Index, Summands of Syzygies and Linearity in Resolutions
Abstract The Burch index is a new invariant of a local ringRwhose positivity implies a kind of linearity in resolutions ofR-modules. We show that ifRhas depth zero and Burch index at least 2, then any non-free 7thR-syzygy contains the residue field as a direct summand. We compute the Burch index in various cases of interest.
more »
« less
- PAR ID:
- 10397596
- Publisher / Repository:
- Springer Science + Business Media
- Date Published:
- Journal Name:
- Bulletin of the Iranian Mathematical Society
- Volume:
- 49
- Issue:
- 2
- ISSN:
- 1017-060X
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Abstract Pulsars in binary systems with strong companion winds can have the magnetopause separating their magnetosphere from the wind located well within their light cylinder. This bow-like enclosure effectively creates a waveguide that confines the pulsar’s electromagnetic fields and can significantly alter its spindown. In this paper, we study the spindown of compressed pulsar magnetospheres in such systems. We parameterize the confinement as the ratio between the equatorial position of the magnetopause (or standoff distance)Rmand the pulsar’s light cylinderRLC. Using particle-in-cell simulations, we quantify the pulsar spindown for a range of compressions,Rm/RLC= 1/3–1, and inclination angles,χ= 0°…90°, between magnetic and rotation axes. Our strongly confined models (Rm/RLC= 1/3) show two distinct limits. Forχ= 0°, the spindown of a compressed pulsar magnetosphere is enhanced by approximately a factor of three compared to an isolated pulsar due to the increased number of open magnetic field lines. Conversely, forχ= 90°, the compressed pulsar spins down at less than 40% of the rate of an isolated reference pulsar due to the mismatch between the pulsar wind stripe wavelength and the waveguide size. We apply our analysis to the 2.77 s oblique rotator (χ= 60°) in the double-pulsar system PSR J0737-3039. With the numerically derived spindown estimate, we constrain its surface magnetic field toB*≈ (7.3 ± 0.2) × 1011G. We discuss the time modulation of its period derivative, the effects of compression on its braking index, and implications for the radio eclipse in PSR J0737-3039.more » « less
-
Summary Spatiotemporal patterns ofSpartina alterniflorabelowground biomass (BGB) are important for evaluating salt marsh resiliency. To solve this, we created the BERM (Belowground Ecosystem Resiliency Model), which estimates monthly BGB (30‐m spatial resolution) from freely available data such as Landsat‐8 and Daymet climate summaries.Our modeling framework relied on extreme gradient boosting, and used field observations from four Georgia salt marshes as ground‐truth data. Model predictors included estimated tidal inundation, elevation, leaf area index, foliar nitrogen, chlorophyll, surface temperature, phenology, and climate data. The final model included 33 variables, and the most important variables were elevation, vapor pressure from the previous four months, Normalized Difference Vegetation Index (NDVI) from the previous five months, and inundation.Root mean squared error for BGB from testing data was 313 g m−2(11% of the field data range), explained variance (R2) was 0.62–0.77. Testing data results were unbiased across BGB values and were positively correlated with ground‐truth data across all sites and years (r = 0.56–0.82 and 0.45–0.95, respectively).BERM can estimate BGB withinSpartina alterniflorasalt marshes where environmental parameters are within the training data range, and can be readily extended through a reproducible workflow. This provides a powerful approach for evaluating spatiotemporal BGB and associated ecosystem function.more » « less
-
Abstract This is the first in a series of papers on the properties of ultradiffuse galaxies (UDGs) in clusters of galaxies. We present an updated catalog of UDGs in the Coma Cluster usingg- andr-band images obtained with Hyper Suprime-Cam (HSC) of the Subaru telescope. We develop a method to find UDGs even in the presence of contaminating objects, such as halos and background galaxies. This study expands upon our previous works that covered about half the area of the Coma Cluster. The HSC observations covered the whole Coma Cluster up to the virial radius and beyond (an area twice as large as the previous studies) and doubled the numbers of UDGs (reff, r≥ 1.5 kpc) and sub-UDGs (1.0 ≤reff, r< 1.5 kpc) to 774 and 729, respectively. The new UDGs show internal properties consistent with those of previous studies (e.g., a Sérsic index of approximately 1), and are distributed across the cluster, with a concentration around the cluster center. The whole cluster coverage clearly revealed an excess of their distribution toward the east to southwest direction along the cluster center, where Coma connects to other large-scale structure, and where a known substructure exists (the NGC 4839 subgroup). The alignment of the UDG distribution along the large-scale structure around Coma supports the interpretation that most of them lie at the distance of the Coma Cluster and the NGC 4839 subgroup.more » « less
-
Abstract Low-mass (≲1.2M⊙) main-sequence stars lose angular momentum over time, leading to a decrease in their magnetic activity. The details of this rotation–activity relation remain poorly understood, however. Using observations of members of the ≈700 Myr old Praesepe and Hyades open clusters, we aim to characterize the rotation–activity relation for different tracers of activity at this age. To complement published data, we obtained new optical spectra for 250 Praesepe stars, new X-ray detections for 10, and new rotation periods for 28. These numbers for Hyads are 131, 23, and 137, respectively. The latter increases the number of Hyads with periods by 50%. We used these data to measure the fractional Hαand X-ray luminosities,LHα/LbolandLX/Lbol, and to calculate Rossby numbersRo. We found that at ≈700 Myr almost all M dwarfs exhibit Hαemission, with binaries having the same overall color–Hαequivalent width distribution as single stars. In theRo–LHα/Lbolplane, unsaturated single stars follow a power law with indexβ= −5.9 ± 0.8 forRo> 0.3. In theRo–LX/Lbolplane, we see evidence for supersaturation for single stars withRo≲ 0.01, following a power law with index , supporting the hypothesis that the coronae of these stars are being centrifugally stripped. We found that the criticalRovalue at which activity saturates is smaller forLX/Lbolthan forLHα/Lbol. Finally, we observed an almost 1:1 relation betweenLHα/LbolandLX/Lbol, suggesting that both the corona and the chromosphere experience similar magnetic heating.more » « less
