331 research outputs found
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 pipelineâin 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 square degrees with approximately
uniform noise. We detected 181 clumps spanning almost three orders of magnitude
in mass (3\Msun \Msun) and with sizes in the range 0.1--1.0 pc.
We find that the clump mass function is well fit with a power law
of the mass with exponent -0.6 (or equivalently ). 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 .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
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