Assigning confidence scores to homoeologs using fuzzy logic.

In polyploid genomes, homoeologs are a specific subtype of homologs, and can be thought of as orthologs between subgenomes. In Orthologous MAtrix, we infer homoeologs in three polyploid plant species: upland cotton (Gossypium hirsutum), rapeseed (Brassica napus), and bread wheat (Triticum aestivum). While we can typically recognize the features of a "good" homoeolog prediction (a consistent evolutionary distance, high synteny, and a one-to-one relationship), none of them is a hard-fast criterion. We devised a novel fuzzy logic-based method to assign confidence scores to each pair of predicted homoeologs. We inferred homoeolog pairs and used the new and improved method to assign confidence scores, which ranged from 0 to 100. Most confidence scores were between 70 and 100, but the distribution varied between genomes. The new confidence scores show an improvement over our previous method and were manually evaluated using a subset from various confidence ranges

OMA 2011: orthology inference among 1000 complete genomes

OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genomes. Initiated in 2004, the project is at its 11th release. It now includes 1000 genomes, making it one of the largest resources of its kind. Here, we describe recent developments in terms of species covered; the algorithmic pipeline—in particular regarding the treatment of alternative splicing, and new features of the web (OMA Browser) and programming interface (SOAP API). In the second part, we review the various representations provided by OMA and their typical applications. The database is publicly accessible at http://omabrowser.org

On the Enhanced Interstellar Scattering Toward B1849+005

(Abridged) This paper reports new Very Large Array (VLA) and Very Long Baseline Array (VLBA) observations of the extragalactic source B1849+005 at frequencies between 0.33 and 15 GHz and the re-analysis of archival VLA observations at 0.33, 1.5, and 4.9 GHz. The structure of this source is complex but interstellar scattering dominates the structure of the central component at least to 15 GHz. An analysis of the phase structure functions of the interferometric visibilities shows the density fluctuations along this line of sight to be anisotropic (axial ratio = 1.3) with a frequency-independent position angle, and having an inner scale of roughly a few hundred kilometers. The anisotropies occur on length scales of order 10^{15} cm (D/5 kpc), which within the context of certain magnetohydrodynamic turbulence theories indicates the length scale on which the kinetic and magnetic energy densities are comparable. A conservative upper limit on the velocity of the scattering material is 1800 km/s. In the 0.33 GHz field of view, there are a number of other sources that might also be heavily scattered. Both B1849+005 and PSR B1849+00 are highly scattered, and they are separated by only 13'. If the lines of sight are affected by the same ``clump'' of scattering material, it must be at least 2.3 kpc distant. However, a detailed attempt to account for the scattering observables toward these sources does not produce a self-consistent set of parameters for such a clump. A clump of H\alpha emission, possibly associated with the H II region G33.418-0.004, lies between these two lines of sight, but it seems unable to account for all of the required excess scattering.Comment: 23 pages, LaTeX2e AASTeX, 13 figures in 14 PostScript files, accepted for publication in Ap

Partial Homology Relations - Satisfiability in terms of Di-Cographs

Directed cographs (di-cographs) play a crucial role in the reconstruction of evolutionary histories of genes based on homology relations which are binary relations between genes. A variety of methods based on pairwise sequence comparisons can be used to infer such homology relations (e.g.\ orthology, paralogy, xenology). They are \emph{satisfiable} if the relations can be explained by an event-labeled gene tree, i.e., they can simultaneously co-exist in an evolutionary history of the underlying genes. Every gene tree is equivalently interpreted as a so-called cotree that entirely encodes the structure of a di-cograph. Thus, satisfiable homology relations must necessarily form a di-cograph. The inferred homology relations might not cover each pair of genes and thus, provide only partial knowledge on the full set of homology relations. Moreover, for particular pairs of genes, it might be known with a high degree of certainty that they are not orthologs (resp.\ paralogs, xenologs) which yields forbidden pairs of genes. Motivated by this observation, we characterize (partial) satisfiable homology relations with or without forbidden gene pairs, provide a quadratic-time algorithm for their recognition and for the computation of a cotree that explains the given relations

The Early Evolution of Massive Stars: Radio Recombination Line Spectra

Velocity shifts and differential broadening of radio recombination lines are used to estimate the densities and velocities of the ionized gas in several hypercompact and ultracompact HII regions. These small HII regions are thought to be at their earliest evolutionary phase and associated with the youngest massive stars. The observations suggest that these HII regions are characterized by high densities, supersonic flows and steep density gradients, consistent with accretion and outflows that would be associated with the formation of massive stars.Comment: ApJ in pres

Coordinated thermal and optical observations of Trans-Neptunian object (20000) Varuna from Sierra Nevada

We report on coordinated thermal and optical measurements of trans-Neptunian object (20000) Varuna obtained in January-February 2002, respectively from the IRAM 30-m and IAA 1.5 m telescopes. The optical data show a lightcurve with a period of 3.176+/-0.010 hr, a mean V magnitude of 20.37+/-0.08 and a 0.42+/-0.01 magnitude amplitude. They also tentatively indicate that the lightcurve is asymmetric and double-peaked. The thermal observations indicate a 1.12+/-0.41 mJy flux, averaged over the object's rotation. Combining the two datasets, we infer that Varuna has a mean 1060(+180/-220) km diameter and a mean 0.038(+0.022/-0.010) V geometric albedo, in general agreement with an earlier determination using the same technique.Comment: Accepted for publication in Astronomy & Astrophysics (7 pages, including 3 figures

Subarcsecond Submillimeter Imaging of the Ultracompact HII Region G5.89-0.39

We present the first subarcsecond submillimeter images of the enigmatic ultracompact HII region (UCHII) G5.89-0.39. Observed with the SMA, the 875 micron continuum emission exhibits a shell-like morphology similar to longer wavelengths. By using images with comparable angular resolution at five frequencies obtained from the VLA archive and CARMA, we have removed the free-free component from the 875 micron image. We find five sources of dust emission: two compact warm objects (SMA1 and SMA2) along the periphery of the shell, and three additional regions further out. There is no dust emission inside the shell, supporting the picture of a dust-free cavity surrounded by high density gas. At subarcsecond resolution, most of the molecular gas tracers encircle the UCHII region and appear to constrain its expansion. We also find G5.89-0.39 to be almost completely lacking in organic molecular line emission. The dust cores SMA1 and SMA2 exhibit compact spatial peaks in optically-thin gas tracers (e.g. 34SO2), while SMA1 also coincides with 11.9 micron emission. In CO(3-2), we find a high-velocity north/south bipolar outflow centered on SMA1, aligned with infrared H2 knots, and responsible for much of the maser activity. We conclude that SMA1 is an embedded intermediate mass protostar with an estimated luminosity of 3000 Lsun and a circumstellar mass of ~1 Msun. Finally, we have discovered an NH3 (3,3) maser 12 arcsec northwest of the UCHII region, coincident with a 44 GHz CH3OH maser, and possibly associated with the Br gamma outflow source identified by Puga et al. (2006).Comment: 41 pages, 11 figures, published in The Astrophysical Journal (2008) Volume 680, Issue 2, pp. 1271-1288. An error in the registration of the marker positions in Figure 11 has been corrected in this versio

Uncertain groupings: probabilistic combination of grouping data

Probabilistic approaches for data integration have much potential. We view data integration as an iterative process where data understanding gradually increases as the data scientist continuously refines his view on how to deal with learned intricacies like data conflicts. This paper presents a probabilistic approach for integrating data on groupings. We focus on a bio-informatics use case concerning homology. A bio-informatician has a large number of homology data sources to choose from. To enable querying combined knowledge contained in these sources, they need to be integrated. We validate our approach by integrating three real-world biological databases on homology in three iterations

Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python.

The Orthologous Matrix (OMA) is a well-established resource to identify orthologs among many genomes. Here, we present two recent additions to its programmatic interface, namely a REST API, and user-friendly R and Python packages called OmaDB. These should further facilitate the incorporation of OMA data into computational scripts and pipelines. The REST API can be freely accessed at https://omabrowser.org/api. The R OmaDB package is available as part of Bioconductor at http://bioconductor.org/packages/OmaDB/, and the omadb Python package is available from the Python Package Index (PyPI) at https://pypi.org/project/omadb/

CARMA CO(J = 2 - 1) Observations of the Circumstellar Envelope of Betelgeuse

We report radio interferometric observations of the 12C16O 1.3 mm J = 2-1 emission line in the circumstellar envelope of the M supergiant Alpha Ori and have detected and separated both the S1 and S2 flow components for the first time. Observations were made with the Combined Array for Research in Millimeter-wave Astronomy (CARMA) interferometer in the C, D, and E antenna configurations. We obtain good u-v coverage (5-280 klambda) by combining data from all three configurations allowing us to trace spatial scales as small as 0.9\arcsec over a 32\arcsec field of view. The high spectral and spatial resolution C configuration line profile shows that the inner S1 flow has slightly asymmetric outflow velocities ranging from -9.0 km s-1 to +10.6 km s-1 with respect to the stellar rest frame. We find little evidence for the outer S2 flow in this configuration because the majority of this emission has been spatially-filtered (resolved out) by the array. We also report a SOFIA-GREAT CO(J= 12-11) emission line profile which we associate with this inner higher excitation S1 flow. The outer S2 flow appears in the D and E configuration maps and its outflow velocity is found to be in good agreement with high resolution optical spectroscopy of K I obtained at the McDonald Observatory. We image both S1 and S2 in the multi-configuration maps and see a gradual change in the angular size of the emission in the high absolute velocity maps. We assign an outer radius of 4\arcsec to S1 and propose that S2 extends beyond CARMA's field of view (32\arcsec at 1.3 mm) out to a radius of 17\arcsec which is larger than recent single-dish observations have indicated. When azimuthally averaged, the intensity fall-off for both flows is found to be proportional to R^{-1}, where R is the projected radius, indicating optically thin winds with \rho \propto R^{-2}.Comment: 11 pages, 8 figures To be published in the Astronomical Journal (Received 2012 February 10; accepted 2012 May 25