PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information

PRofile ALIgNEment (PRALINE) is a fully customizable multiple sequence alignment application. In addition to a number of available alignment strategies, PRALINE can integrate information from database homology searches to generate a homology-extended multiple alignment. PRALINE also provides a choice of seven different secondary structure prediction programs that can be used individually or in combination as a consensus for integrating structural information into the alignment process. The program can be used through two separate interfaces: one has been designed to cater to more advanced needs of researchers in the field, and the other for standard construction of high confidence alignments. The web-based output is designed to facilitate the comprehensive visualization of the generated alignments by means of five default colour schemes based on: residue type, position conservation, position reliability, residue hydrophobicity and secondary structure, depending on the options set. A user can also define a custom colour scheme by selecting which colour will represent one or more amino acids in the alignment. All generated alignments are also made available in the PDF format for easy figure generation for publications. The grouping of sequences, on which the alignment is based, can also be visualized as a dendrogram. PRALINE is available at

Scooby-domain: prediction of globular domains in protein sequence

Scooby-domain (sequence hydrophobicity predicts domains) is a fast and simple method to identify globular domains in protein sequence, based on the observed lengths and hydrophobicities of domains from proteins with known tertiary structure. The prediction method successfully identifies sequence regions that will form a globular structure and those that are likely to be unstructured. The method does not rely on homology searches and, therefore, can identify previously unknown domains for structural elucidation. Scooby-domain is available as a Java applet at . It may be used to visualize local properties within a protein sequence, such as average hydrophobicity, secondary structure propensity and domain boundaries, as well as being a method for fast domain assignment of large sequence sets

Design optimization of field-plate assisted RESURF devices

A mathematical model for optimizing the 2-D potential distribution in the drift region of field-plate (FP)-assisted RESURF devices (Fig. 1) is presented. The proposed model extends earlier work [1-2] by including top-bottom dielectric asymmetry (typical in SOI devices [3]), non-zero field plate potentials VFP and grading of design parameters other than drift region doping. This generally-applicable, TCAD-verified [4], model provides a guideline for optimizing the drain extension in a wide range of FP-assisted RESURF devices

Identifying foldable regions in protein sequence from the hydrophobic signal

Structural genomics initiatives aim to elucidate representative 3D structures for the majority of protein families over the next decade, but many obstacles must be overcome. The correct design of constructs is extremely important since many proteins will be too large or contain unstructured regions and will not be amenable to crystallization. It is therefore essential to identify regions in protein sequences that are likely to be suitable for structural study. Scooby-Domain is a fast and simple method to identify globular domains in protein sequences. Domains are compact units of protein structure and their correct delineation will aid structural elucidation through a divide-and-conquer approach. Scooby-Domain predictions are based on the observed lengths and hydrophobicities of domains from proteins with known tertiary structure. The prediction method employs an A*-search to identify sequence regions that form a globular structure and those that are unstructured. On a test set of 173 proteins with consensus CATH and SCOP domain definitions, Scooby-Domain has a sensitivity of 50% and an accuracy of 29%, which is better than current state-of-the-art methods. The method does not rely on homology searches and, therefore, can identify previously unknown domains

Graphical representations and cluster algorithms for critical points with fields

A two-replica graphical representation and associated cluster algorithm is described that is applicable to ferromagnetic Ising systems with arbitrary fields. Critical points are associated with the percolation threshold of the graphical representation. Results from numerical simulations of the Ising model in a staggered field are presented. The dynamic exponent for the algorithm is measured to be less than 0.5.Comment: Revtex, 12 pages with 2 figure

SEQATOMS: a web tool for identifying missing regions in PDB in sequence context.

doi:10.1093/nar/gkn23

Diffusive Thermal Dynamics for the Ising Ferromagnet

We introduce a thermal dynamics for the Ising ferromagnet where the energy variations occurring within the system exhibit a diffusive character typical of thermalizing agents such as e.g. localized excitations. Time evolution is provided by a walker hopping across the sites of the underlying lattice according to local probabilities depending on the usual Boltzmann weight at a given temperature. Despite the canonical hopping probabilities the walker drives the system to a stationary state which is not reducible to the canonical equilibrium state in a trivial way. The system still exhibits a magnetic phase transition occurring at a finite value of the temperature larger than the canonical one. The dependence of the model on the density of walkers realizing the dynamics is also discussed. Interestingly the differences between the stationary state and the Boltzmann equilibrium state decrease with increasing number of walkers.Comment: 9 pages, 14 figures. Accepted for publication on PR