HMMER web server: interactive sequence similarity searching

HMMER is a software suite for protein sequence similarity searches using probabilistic methods. Previously, HMMER has mainly been available only as a computationally intensive UNIX command-line tool, restricting its use. Recent advances in the software, HMMER3, have resulted in a 100-fold speed gain relative to previous versions. It is now feasible to make efficient profile hidden Markov model (profile HMM) searches via the web. A HMMER web server (http://hmmer.janelia.org) has been designed and implemented such that most protein database searches return within a few seconds. Methods are available for searching either a single protein sequence, multiple protein sequence alignment or profile HMM against a target sequence database, and for searching a protein sequence against Pfam. The web server is designed to cater to a range of different user expertise and accepts batch uploading of multiple queries at once. All search methods are also available as RESTful web services, thereby allowing them to be readily integrated as remotely executed tasks in locally scripted workflows. We have focused on minimizing search times and the ability to rapidly display tabular results, regardless of the number of matches found, developing graphical summaries of the search results to provide quick, intuitive appraisement of them

Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction

BACKGROUND: RNA secondary structure prediction methods based on probabilistic modeling can be developed using stochastic context-free grammars (SCFGs). Such methods can readily combine different sources of information that can be expressed probabilistically, such as an evolutionary model of comparative RNA sequence analysis and a biophysical model of structure plausibility. However, the number of free parameters in an integrated model for consensus RNA structure prediction can become untenable if the underlying SCFG design is too complex. Thus a key question is, what small, simple SCFG designs perform best for RNA secondary structure prediction? RESULTS: Nine different small SCFGs were implemented to explore the tradeoffs between model complexity and prediction accuracy. Each model was tested for single sequence structure prediction accuracy on a benchmark set of RNA secondary structures. CONCLUSIONS: Four SCFG designs had prediction accuracies near the performance of current energy minimization programs. One of these designs, introduced by Knudsen and Hein in their PFOLD algorithm, has only 21 free parameters and is significantly simpler than the others

Pengaruh Profitabilitas, Leverage, Struktur Kepemilikan dan Status Perusahaan terhadap Pengungkapan Laporan Keuangan pada Perusahan Manufaktur yang Terdaftar di Bursa Efek Indonesia

Penelitian ini bertujuan untuk menganalisis pengaruh profitabilitas, leverage, struktur kepemilikan dan status Perusahaan terhadap pengungkapan laporan keuangan. Teknik pengambilan sampel yang digunakan adalah random sampling dengan menggunakan rumus slovin, dengan jumlah sampel 58 Perusahaan. Data diperoleh dari Bursa Efek Indonesia dari tahun 2012-2013. Teknik analisis data yang dipergunakan adalah analisis regresi linear berganda. Hasil koefisien determinasi sebesar 0.117 hal ini berarti bahwa besarnya kemampuan variable independen untuk menjelaskan variable devenden adalah 11.7% dan sisanya sebesar 88.3% dipengaruhi oleh faktor-faktor lain yang tidak dimasukkan dalam model regresi. Berdasarkan hasil analisis regresi uji F menunjukkan bahwa profitabilitas (ROA), leverage (DER), kepemilikan institusional dan status Perusahaan secara simultan berpengaruh positif dan signifikan terhadap pengungkapan laporan keuangan pada Perusahaan manufaktur yang terdaftar di Bursa Efek Indonesia. Berdasarkan hasil analisis regresi uji t menunjukkan bahwa profitabilitas (ROA) berpengaruh negatif dan signifikan, leverage (DER) berpengaruh positif dan tidak signifikan, kepemilikan institusional memiliki pengaruh negatif dan signifikan, dan status Perusahaan memiliki pengaruh positif dan tidak signifikan terhadap pengungkapan laporan keuangan pada Perusahaan manufaktur yang terdaftar di Bursa Efek Indonesia. Berdasarkan hasil penelitian dapat disimpulkan bahwa profitabilitas, leverage, struktur kepemilikan dan status Perusahaan berpengaruh terhadap lengkap atau tidaknya pengungkapan laporan keuangan. Saran yang diberikan kepada peneliti selanjutnya hendaknya menggunakan variabel-variabel lain yang mempengaruhi pengungkapan laporan keuagan

Measuring frequency fluctuations in nonlinear nanomechanical resonators

Advances in nanomechanics within recent years have demonstrated an always expanding range of devices, from top-down structures to appealing bottom-up MoS$_2$ and graphene membranes, used for both sensing and component-oriented applications. One of the main concerns in all of these devices is frequency noise, which ultimately limits their applicability. This issue has attracted a lot of attention recently, and the origin of this noise remains elusive up to date. In this Letter we present a very simple technique to measure frequency noise in nonlinear mechanical devices, based on the presence of bistability. It is illustrated on silicon-nitride high-stress doubly-clamped beams, in a cryogenic environment. We report on the same $T/f$ dependence of the frequency noise power spectra as reported in the literature. But we also find unexpected {\it damping fluctuations}, amplified in the vicinity of the bifurcation points; this effect is clearly distinct from already reported nonlinear dephasing, and poses a fundamental limit on the measurement of bifurcation frequencies. The technique is further applied to the measurement of frequency noise as a function of mode number, within the same device. The relative frequency noise for the fundamental flexure $\delta f/f_0$ lies in the range $0.5 - 0.01~$ppm (consistent with literature for cryogenic MHz devices), and decreases with mode number in the range studied. The technique can be applied to {\it any types} of nano-mechanical structures, enabling progresses towards the understanding of intrinsic sources of noise in these devices.Comment: Published 7 may 201

Polarization selection rules for inter-Landau level transitions in epitaxial graphene revealed by infrared optical Hall effect

We report on polarization selection rules of inter-Landau level transitions using reflection-type optical Hall effect measurements from 600 to 4000 cm-1 on epitaxial graphene grown by thermal decomposition of silicon carbide. We observe symmetric and anti-symmetric signatures in our data due to polarization preserving and polarization mixing inter-Landau level transitions, respectively. From field-dependent measurements we identify that transitions in decoupled graphene mono-layers are governed by polarization mixing selection rules, whereas transitions in coupled graphene mono-layers are governed by polarization preserving selection rules. The selection rules may find explanation by different coupling mechanisms of inter-Landau level transitions with free charge carrier magneto-optic plasma oscillations

Membrane amplitude and triaxial stress in twisted bilayer graphene deciphered using first-principles directed elasticity theory and scanning tunneling microscopy

Twisted graphene layers produce a moir\'e pattern (MP) structure with a predetermined wavelength for given twist angle. However, predicting the membrane corrugation amplitude for any angle other than pure AB-stacked or AA-stacked graphene is impossible using first-principles density functional theory (DFT) due to the large supercell. Here, within elasticity theory we define the MP structure as the minimum energy configuration, thereby leaving the height amplitude as the only unknown parameter. The latter is determined from DFT calculations for AB and AA stacked bilayer graphene in order to eliminate all fitting parameters. Excellent agreement with scanning tunneling microscopy (STM) results across multiple substrates is reported as function of twist angle.Comment: to appear in Phys. Rev.