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

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

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

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

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

The very flat radio - millimetre spectrum of Cygnus X-1

We present almost-simultaneous detections of Cygnus X-1 in the radio and mm regimes, obtained during the low/hard X-ray state. The source displays a flat spectrum between 2 and 220 GHz, with a spectral index flatter than 0.15 (3sigma). There is no evidence for either a low- or high-frequency cut-off, but in the mid-infrared (~30 microns) thermal emission from the OB-type companion star becomes dominant. The integrated luminosity of this flat-spectrum emission in quiescence is > 2 x 10^{31} erg/s (2 x 10^{24} W). Assuming the emission originates in a jet for which non-radiative (e.g. adiabatic expansion) losses dominate, this is a very conservative lower limit on the power required to maintain the jet. A comparison with Cyg X-3 and GRS 1915+105, the other X-ray binaries for which a flat spectrum at shorter than cm wavelengths has been observed, shows that the jet in Cyg X-1 is significantly less luminous and less variable, and is probably our best example to date of a continuous, steady, outflow from an X-ray binary. The emissive mechanism reponsible for such a flat spectral component remains uncertain. Specifically, we note that the radio-mm spectra observed from these X-ray binaries are much flatter than those of the `flat-spectrum' AGN, and that existing models of synchrotron emission from partially self-absorbed radio cores, which predict a high-frequency cut-off in the mm regime, are not directly applicable.Comment: Accepted for publication in MNRA

Massive Clumps in the NGC 6334 Star Forming Region

We report observations of dust continuum emission at 1.2 mm toward the star forming region NGC 6334 made with the SEST SIMBA bolometer array. The observations cover an area of $\sim 2$ square degrees with approximately uniform noise. We detected 181 clumps spanning almost three orders of magnitude in mass (3\Msun$-6\times10^3$ \Msun) and with sizes in the range 0.1--1.0 pc. We find that the clump mass function $dN/d\log M$ is well fit with a power law of the mass with exponent -0.6 (or equivalently $dN/dM \propto M^{-1.6}$). The derived exponent is similar to those obtained from molecular line emission surveys and is significantly different from that of the stellar initial mass function. We investigated changes in the mass spectrum by changing the assumptions on the temperature distribution of the clumps and on the contribution of free-free emission to the 1.2 mm emission, and found little changes on the exponent. The Cumulative Mass Distribution Function is also analyzed giving consistent results in a mass range excluding the high-mass end where a power-law fit is no longer valid. The masses and sizes of the clumps observed in NGC 6334 indicate that they are not direct progenitors of stars and that the process of fragmentation determines the distribution of masses later on or occurs at smaller spatial scales. The spatial distribution of the clumps in NGC 6334 reveals clustering which is strikingly similar to that exhibited by young stars in other star forming regions. A power law fit to the surface density of companions gives $\Sigma\propto \theta^{-0.62}$.Comment: 16 pages, 11 figures, 4 tables. To appear in the Astrophysical Journa

The Mid-Infrared Colors of the ISM and Extended Sources at the Galactic Center

A mid-infrared (3.6-8 um) survey of the Galactic Center has been carried out with the IRAC instrument on the Spitzer Space Telescope. This survey covers the central 2x1.4 degree (~280x200 pc) of the Galaxy. At 3.6 and 4.5 um the emission is dominated by stellar sources, the fainter ones merging into an unresolved background. At 5.8 and 8 um the stellar sources are fainter, and large-scale diffuse emission from the ISM of the Galaxy's central molecular zone becomes prominent. The survey reveals that the 8 to 5.8 um color of the ISM emission is highly uniform across the surveyed region. This uniform color is consistent with a flat extinction law and emission from polycyclic aromatic hydrocarbons (PAHs). Models indicate that this broadband color should not be expected to change if the incident radiation field heating the dust and PAHs is <10^4 times that of the solar neighborhood. The few regions with unusually red emission are areas where the PAHs are underabundant and the radiation field is locally strong enough to heat large dust grains to produce significant 8 um emission. These red regions include compact H II regions, Sgr B1, and wider regions around the Arches and Quintuplet Clusters. In these regions the radiation field is >10^4 times that of the solar neighborhood. Other regions of very red emission indicate cases where thick dust clouds obscure deeply embedded objects or very early stages of star formation.Comment: 37 pages, 15 Postscript figures (low resolution). Accepted for publication in the Ap

Interferometric imaging of the sulfur-bearing molecules H2S, SO and CS in comet C/1995 O1 (Hale-Bopp)

We present observations of rotational lines of H2S, SO and CS performed in comet C/1995 O1 (Hale-Bopp) in March 1997 with the Plateau de Bure interferometer (IRAM). The observations provide informations on the spatial and velocity distributions of these molecules. They can be used to constrain their photodissociation rate and their origin. We use a radiative transfer code which allows us to compute synthetic line profiles and interferometric maps, to be compared to the observations. Both single-dish spectra and interferometric spectral maps show a day/night asymmetry in the outgassing. From the analysis of the spectral maps, including the astrometry, we show that SO and CS present in addition a jet-like structure that may be the gaseous counterpart of the dust high-latitude jet observed in optical images. A CS rotating jet is also observed. Using the astrometry provided by continuum radio maps obtained in parallel, we conclude that there is no need to invoke of nongravitational forces acting on this comet, and provide an updated orbit. The radial extension of H2S is found to be consistent with direct release from the nucleus. SO displays an extended radial distribution. Assuming that SO2 is the parent of SO, the photodissociation rate of SO is measured to be 1.5 E-4 s-1 at 1 AU from the Sun. This is lower than most laboratory-based estimates and may suggest that SO is not solely produced by SO2 photolysis. From the observations of J(2-1) and J(5-4) CS lines, we deduce a CS photodissociation rate of 1 to 5 E-5 s-1. The photodissociation rate of CS2, the likely parent of CS, cannot be constrained due to insufficient resolution, but our data are consistent with published values. These observations illustrate the cometary science that will be performed with the future ALMA interferometer.Comment: Accepted for publication in Astronomy & Astrophysic

Re-analysis of the radio luminosity function of Galactic HII regions

We have re-analyzed continuum and recombination lines radio data available in the literature in order to derive the luminosity function (LF) of Galactic HII regions. The study is performed by considering the first and fourth Galactic quadrants independently. We estimate the completeness level of the sample in the fourth quadrant at 5 Jy, and the one in the first quadrant at 2 Jy. We show that the two samples (fourth or first quadrant) include, as well as giant and super-giant HII regions, a significant number of sub-giant sources. The LF is obtained, in each Galactic quadrant, with a generalized Schmidt's estimator using an effective volume derived from the observed spatial distribution of the considered HII regions. The re-analysis also takes advantage of recently published ancillary absorption data allowing to solve the distance ambiguity for several objects. A single power-law fit to the LFs retrieves a slope equal to -2.23+/-0.07 (fourth quadrant) and to -1.85+/-0.11 (first quadrant). We also find marginal evidence of a luminosity break at L_knee = 10^23.45 erg s^(-1) Hz^(-1) for the LF in the fourth quadrant. We convert radio luminosities into equivalent H_alpha and Lyman continuum luminosities to facilitate comparisons with extra-galactic studies. We obtain an average total HII regions Lyman continuum luminosity of 0.89 +/- 0.23 * 10^(53) sec^(-1), corresponding to 30% of the total ionizing luminosity of the Galaxy.Comment: accepted for publication in Ap