HomologyPlot: Searching for homology to a family of proteins using a database of unique conserved patterns

Summary A new database of conserved amino acid residues is derived from the multiple sequence alignment of over 84 families of protein sequences that have been reported in the literature. This database contains sequences of conserved hydrophobic core patterns which are probably important for structure and function, since they are conserved for most sequences in that family. This database differs from other single-motif or signature databases reported previously, since it contains multiple patterns for each family. The new database is used to align a new sequence with the conserved regions of a family. This is analogous to reports in the literature where multiple sequence alignments are used to improve a sequence alignment. A program called Homology-Plot (suitable for IBM or compatible computers) uses this database to find homology of a new sequence to a family of protein sequences. There are several advantages to using multiple patterns. First, the program correctly identifies a new sequence as a member of a known family. Second, the search of the entire database is rapid and requires less than one minute. This is similar to performing a multiple sequence alignment of a new sequence to all of the known protein family sequences. Third, the alignment of a new sequence to family members is reliable and can reproduce the alignment of conserved regions already described in the literature. The speed and efficiency of this method is enhanced, since there is no need to score for insertions or deletions as is done in the more commonly used sequence alignment methods. In this method only the patterns are aligned. HomologyPlot also provides general information on each family, as well as a listing of patterns in a family.     

Aligning Text and Phonemes for Speech Technology Applications Using an EM-Like Algorithm

A common requirement in speech technology is to align two different symbolic representations of the same linguistic ‘message’. For instance, we often need to align letters of words listed in a dictionary with the corresponding phonemes specifying their pronunciation. As dictionaries become ever bigger, manual alignment becomes less and less tenable yet automatic alignment is a hard problem for a language like English. In this paper, we describe the use of a form of the expectation-maximization (EM) algorithm to learn alignments of English text and phonemes, starting from a variety of initializations. We use the British English Example Pronunciation (BEEP) dictionary of almost 200,000 words in this work. The quality of alignment is difficult to determine quantitatively since no ‘gold standard’ correct alignment exists. We evaluate the success of our algorithm indirectly from the performance of a pronunciation by analogy system using the aligned dictionary data as a knowledge base for inferring pronunciations. We find excellent performance—the best so far reported in the literature. There is very little dependence on the start point for alignment, indicating that the EM search space is strongly convex. Since the aligned BEEP dictionary is a potentially valuable resource, it is made freely available for research use.     

Protein alignment: Exact versus approximate. An illustration

We illustrate solving the protein alignment problem exactly using the algorithm VESPA (very efficient search for protein alignment). We have compared our result with the approximate solution obtained with BLAST (basic local alignment search tool) software, which is currently the most widely used for searching for protein alignment. We have selected human and mouse proteins having around 170 amino acids for comparison. The exact solution has found 78 pairs of amino acids, to which one should add 17 individual amino acid alignments giving a total of 95 aligned amino acids. BLAST has identified 64 aligned amino acids which involve pairs of more than two adjacent amino acids. However, the difference between the two outputs is not as large as it may appear, because a number of amino acids that are adjacent have been reported by BLAST as single amino acids. So if one counts all amino acids, whether isolated (single) or in a group of two and more amino acids, then the count for BLAST is 89 and for VESPA is 95, a difference of only six. © 2015 Wiley Periodicals, Inc.     

Different approaches toward an automatic structural alignment of drug molecules: Applications to sterol mimics,thrombin and thermolysin inhibitors

Summary A relative comparison of the binding properties of different drug molecules requires their mutual superposition with respect to various alignment criteria. In order to validate the results of different alignment methods, the crystallographically observed binding geometries of ligands in the pocket of a common protein receptor have been used. The alignment function in the program SEAL that calculates the mutual superposition of molecules has been optimized with respect to these references. Across the reference data set, alignments could be produced that show mean rms deviations of approximately 1 Å compared to the experimental situation. For structures with obvious skeletal similarities a multiple-flexible fit, linking common pharmacophoric groups by virtual springs, has been incorporated into the molecular mechanics program MOMO. In order to combine conformational searching with comparative alignments, the optimized SEAL approach has been applied to sets of conformers generated by MIMUMBA, a program for conformational analysis. Multiple-flexible fits have been calculated for inhibitors of ergosterol biosynthesis. Sets of different thrombin and thermolysin inhibitors have been conformationally analyzed and subsequently aligned by a combined MIMUMBA/SEAL approach. Since for these examples crystallographic data on their mutual alignment are available, an objective assessment of the computed results could be performed. Among the generated conformers, one geometry could be selected for the thrombin and thermolysin inhibitors that approached reasonably well the experimentally observed alignment.     

An adaptive and iterative algorithm for refining multiple sequence alignment

Multiple sequence alignment is a basic tool in computational genomics. The art of multiple sequence alignment is about placing gaps. This paper presents a heuristic algorithm that improves multiple protein sequences alignment iteratively. A consistency-based objective function is used to evaluate the candidate moves. During the iterative optimization, well-aligned regions can be detected and kept intact. Columns of gaps will be inserted to assist the algorithm to escape from local optimal alignments. The algorithm has been evaluated using the BAliBASE benchmark alignment database. Results show that the performance of the algorithm does not depend on initial or seed alignments much. Given a perfect consistency library, the algorithm is able to produce alignments that are close to the global optimum. We demonstrate that the algorithm is able to refine alignments produced by other software, including ClustalW, SAGA and T-COFFEE. The program is available upon request.     

MolAlign: an algorithm for aligning multiple small molecules

In small molecule drug discovery projects, the receptor structure is not always available. In such cases it is enormously useful to be able to align known ligands in the way they bind in the receptor. Here we shall present an algorithm for the alignment of multiple small molecule ligands. This algorithm takes pre-generated conformers as input, and proposes aligned assemblies of the ligands. The algorithm consists of two stages: the first stage is to perform alignments for each pair of ligands, the second stage makes use of the results from the first stage to build up multiple ligand alignment assemblies using a novel iterative procedure. The scoring functions are improved versions of the one mentioned in our previous work. We have compared our results with some recent publications. While an exact comparison is impossible, it is clear that our algorithm is fast and produces very competitive results.     

MSAID: multiple sequence alignment based on a measure of information discrepancy

We propose an algorithm of global multiple sequence alignment that is based on a measure of what we call information discrepancy. The algorithm follows a progressive alignment iteration strategy that makes use of what we call a function of degree of disagreement (FDOD). MSAID begins with distance calculation of pairwise sequences, based on FDOD as a numerical scoring measure. In the next step, the resulting distance matrix is used to construct a guide tree via the neighbor-joining method. The tree is then used to produce a multiple alignment. Current alignment is next used to produce a new matrix and a new tree (with FDOD scoring measure again). This iterative process continues until convergence criteria (or a stopping rule) are satisfied. MSAID was tested and compared with other prior methods by using reference alignments from BAliBASE 2.01. For the alignments with no large N/C-terminal extensions or internal insertions MSAID received the top overall average in the tests. Moreover, the results of testing indicate that MSAID performs as well as other alignment methods with an occasional tendency to perform better than these prior techniques. We, therefore, believe that MSAID is a solid and reliable method of choice, which is often (if not always) superior to other global alignment techniques.     

4D-QSAR analysis of a series of antifungal p450 inhibitors and 3D-pharmacophore comparisons as a function of alignment

A training set of 55 antifungal p450 analogue inhibitors was used to construct receptor-independent four-dimensional quantitative structure-activity relationship (RI 4D-QSAR) models. Ten different alignments were used to build the models, and one alignment yields a significantly better model than the other alignments. Two different methodologies were used to measure the similarity of the best 4D-QSAR models of each alignment. One method compares the residual of fit between pairs of models using the cross-correlation coefficient of their residuals of fit as a similarity measure. The other method compares the spatial distributions of the IPE types (3D-pharmacophores) of pairs of 4D-QSAR models from different alignments. Optimum models from several different alignments have nearly the same correlation coefficients, r(2), and cross-validation correlation coefficients, xv-r(2), yet the 3D-pharmacophores of these models are very different from one another. The highest 3D-pharmacophore similarity correlation coefficient between any pair of 4D-QSAR models from the 10 alignments considered is only 0.216. However, the best 4D-QSAR models of each alignment do contain some proximate common pharmacorphore sites. A test set of 10 compounds was used to validate the predictivity of the best 4D-QSAR models of each alignment. The "best" model from the 10 alignments has the highest predictivity. The inferred active sites mapped out by the 4D-QSAR models suggest that hydrogen bond interactions are not prevalent when this class of P450 analogue inhibitors binds to the receptor active site. This feature of the 4D-QSAR models is in agreement with the crystal structure results that indicate no ligand-receptor hydrogen bonds are formed.     

Testing homology with Contact Accepted mutatiOn (CAO): a contact-based Markov model of protein evolution

Point Accepted Mutation (PAM) is the Markov model of amino acid replacements in proteins introduced by Dayhoff and her co-workers (Dayhoff et al., 1978). The PAM matrices and other matrices based on the PAM model have been widely accepted as the standard scoring system of protein sequence similarity in protein sequence alignment tools. Here, we present Contact Accepted mutatiOn (CAO), a Markov model of protein residue contact mutations. The CAO model simulates the interchanging of structurally defined side-chain contacts, and introduces additional structural information into protein sequence alignments. Therefore, similarities between structurally conserved sequences can be detected even without apparent sequence similarity. CAO has been benchmarked on the HOMSTRAD database and a subset of the CATH database, by comparing sequence alignments with reference alignments derived from structural superposition. CAO yields scores that reflect coherently the structural quality of sequence alignments, which has implications particularly for homology modelling and threading techniques.     

Evaluation of alignment methods and data pretreatments on the determination of the most important peaks for the discrimination of coffee varieties Arabica and Robusta using gas chromatography-mass spectroscopy

Coffee samples were analyzed by GC/MS in order to determine the most important peaks for the discrimination of the varieties Arabica and Robusta. The resulting peak tables from chromatographic analysis were aligned and pretreated before being submitted to multivariate analysis. A rapid and easy-to-perform peak alignment procedure, which does not require advanced programming skills to use, was compared with the tedious manual alignment procedure. The influence of three types of data pretreatment, normalization, logarithmic and square root transformations and their combinations, on the variables selected as most important by the regression coefficients of partial least squares-discriminant analysis (PLS-DA), are shown. Test samples different from those used in the calibration and comparison with the substances already known as being responsible for Arabica and Robusta coffees discrimination were used to determine the best pretreatments for both datasets. The data pretreatment consisting of square root transformation followed by normalization (RN) was chosen as being the most appropriate. The results obtained showed that the much quicker automated aligned method could be used as a substitute for the manually aligned method, allowing all the peaks in the chromatogram to be used for multivariate analysis.     

Liquid crystals alignment with PbS nanosculptured thin films

Lead sulphide (PbS) nano-sculptured thin films (nSTFs) are prepared for the first time using glancing angle deposition technique by physical vapour deposition process. An anisotropic morphology is obtained, which provides an orientational effect. Due to this anisotropic nature of PbS nSTF an attempt has been made to check its effect on the alignment of nematic liquid crystals (LCs). Two different LC devices were fabricated, that is, anti-parallel aligned or electrically-controlled birefringence and hybrid twisted nematic. It is noticed that in both types of devices, good alignment is obtained with high extinction and contrast. A significant effect of these alignments on the electro-optic properties of the LC is reported such as the threshold voltage, response time and contrast ratio.     

The alignment of nematic liquid crystals on photolithographic micro-groove patterns

The alignment of nematic liquid crystals on micro-groove patterns was studied. It has been found that the order of the alignments is determined by the edge shape, spacing, and line pitch of the micro-groove patterns. On coarse patterns, with pitches greater than 2 μm, striped patterns of the liquid crystal alignment were observed using polarized light which manifested different orientations of the liquid crystals on the top, edge, and bottom of the grooves, respectively. On fine patterns, with pitches less than 2 μm, a uniform device-quality alignment has been realized, with which twisted nematic cells were constructed in combination with the rubbed alignment layer on the opposite substrate. Their viewing angle characteristics and tilt orientations of the director were also investigated.     

Very efficient search for nucleotide alignments

We describe a very efficient search for nucleotide alignments, which is analogous to the novel very efficient search for protein alignment. Just as it has been the case with the alignment of proteins, based on 20 × 20 adjacency matrices for amino acids, obtained from a superposition of labeled amino acids adjacency matrices for the proteins considered, one can construct labeled matrices of size 4 × 4, listing adjacencies of nucleotides in DNA sequence. The matrix elements correspond to 16 pairs of adjacent nucleotides. To obtain DNA alignments, one combines information in the corresponding matrices for a pair of DNA nucleotides. Matrices are obtained by insertion of the sequential labels for pairs of nucleotides in the corresponding cells of the 4 × 4 tables. When two such matrices are superimposed, one can identify all segments in two DNA sequences, which are shifted relative to one another by the same amount in either direction, without using trial‐and‐error displacements of the two sequences one relative to the other to find local nucleotide alignments. © 2012 Wiley Periodicals, Inc.     

The alignment of nematic liquid crystals on photolithographic micro-groove patterns

Abstract

The alignment of nematic liquid crystals on micro-groove patterns was studied. It has been found that the order of the alignments is determined by the edge shape, spacing, and line pitch of the micro-groove patterns. On coarse patterns, with pitches greater than 2 μm, striped patterns of the liquid crystal alignment were observed using polarized light which manifested different orientations of the liquid crystals on the top, edge, and bottom of the grooves, respectively. On fine patterns, with pitches less than 2 μm, a uniform device-quality alignment has been realized, with which twisted nematic cells were constructed in combination with the rubbed alignment layer on the opposite substrate. Their viewing angle characteristics and tilt orientations of the director were also investigated.     

Real-time target selection optimization to enhance alignment of gas chromatograms

An improved method for real-time selection of the target for the alignment of gas chromatographic data is described. Further outlined is a simple method to determine the accuracy of the alignment procedure. The target selection method proposed uses a moving window of aligned chromatograms to generate a target, herein referred to as the window target method (WTM). The WTM was initially tested using a series of 100 simulated chromatograms, and additionally evaluated using a series of 55 diesel fuel gas chromatograms obtained with four fuel samples. The WTM was evaluated via a comparison to a related method (the nearest neighbor method (NNM)). The results using the WTM with simulated chromatograms showed a significant improvement in the correlation coefficient and the accuracy of alignment when compared to the alignments performed using the NNM. A significant improvement in real-time alignment accuracy, as assessed by a correlation coefficient metric, was achieved with the WTM (starting at ∼1.0 and declining to only ∼0.985 for the 100th sample), relative to the NNM (starting at ∼1.0 and declining to ∼0.4 for the 100th sample) for the simulated chromatogram study. The results determined when using the WTM with the diesel fuels also showed an improvement in correlation coefficient and accuracy of the within-class alignments as compared to the results obtained from the NNM. In practice, the WTM could be applied to the real-time analysis of process and feedstock industrial streams to enable real-time decision making from the more precisely aligned chromatographic data.     

CGEMA and VGAP: a Colour Graphics Editor for Multiple Alignment using a Variable GAP penalty. Application to the muscarinic acetylcholine receptor

Summary Today, more than 40 protein amino acid (AA) sequences of membrane receptors coupled to guanine nucleotide binding proteins (G-proteins) are available. For those working in the field of medicinal chemistry, these sequences present a new type of information that should be taken into consideration. To make maximal use of sequence data it is essential to be able to compare different protein sequences in a similar way to that used for small molecules. A prerequisite, however, is the availability of a processing environment that enables one to handle sequences in an easy way, both by hand and by computer. In order to meet these ends, the package CGEMA (Colour Graphics Editor for Multiple Alignment) was developed in our laboratory. The programme uses a user-definable colour coding for the different AAs. Sequences can be aligned by hand or by computer, using VGAP, and both approaches can be combined. VGAP is a novel in-house written alignment programme with a variable gap penalty that also handles consecutive alignments using one sequence as a probe. In addition, secondary structure prediction tools are available.From the 20 protein sequences, available for the muscarinic acetylcholine receptor, 13 different sequences were selected, covering the subtypes m1 to m5. By comparing the sequences, two major groups are revealed that correspond to those found by considering the transducing system coupled to the various receptor subtypes. Different parts of the protein sequences are identified as characterizing the subtype and binding the ligands, respectively.     

Real-time assessment of carbon nanotube alignment in a polymer matrix under an applied electric field via polarized Raman spectroscopy

A technique has been developed utilizing polarized Raman spectroscopy to measure alignment of carbon nanotubes in situ in a polymer matrix under an applied electric field. Previous studies of alignment have been restricted to optically transparent solvents or polymerized specimens that prevent accurate analyses of alignment dynamics in polymers. The effects of electric field strength on the degree of alignment and the time to achieve an aligned state are discussed. The use of in situ, real-time polarized Raman spectroscopy provides a non-invasive technique for assessing carbon nanotube alignment, which can assist in determining processing conditions to improve the mechanical and electrical properties of aligned nanocomposites.     

Alignment of capillary electrophoresis–mass spectrometry datasets using accurate mass information

Capillary electrophoresis–mass spectrometry (CE–MS) is a powerful technique for the analysis of small soluble compounds in biological fluids. A major drawback of CE is the poor migration time reproducibility, which makes it difficult to combine data from different experiments and correctly assign compounds. A number of alignment algorithms have been developed but not all of them can cope with large and irregular time shifts between CE–MS runs. Here we present a genetic algorithm designed for alignment of CE–MS data using accurate mass information. The utility of the algorithm was demonstrated on real data, and the results were compared with one of the existing packages. The new algorithm showed a significant reduction of elution time variation in the aligned datasets. The importance of mass accuracy for the performance of the algorithm was also demonstrated by comparing alignments of datasets from a standard time-of-flight (TOF) instrument with those from the new ultrahigh resolution TOF maXis (Bruker Daltonics).     

Novel alignment mechanism of liquid crystal on a hydrogenated amorphous silicon oxide

The mechanism of liquid crystal (LC) alignment has been investigated during the last few decades for inorganic materials as well as for organic materials; however, it has not been clearly confirmed for some alignment materials. Inorganic alignment materials such as amorphous silicon oxide (a-SiOx) and hydrogenated amorphous silicon oxide (a-SiOx:H) are deposited on indium tin oxide (ITO) films on glass by reactive sputtering deposition. After deposition, the inorganic alignment materials are irradiated using an Ar+ ion beam (IB) for LC alignment. On the basis of the experimental results, a-SiOx films deposited by the sputtering do not align the LC, but a-SiOx:H films treated with varying IB energies, IB incident angles, IB doses, and IB irradiation times have excellent alignment properties and electrooptical properties, identical to those of polyimide (PI). These results imply that inorganic alignment layers irradiated by IB can be adopted as an LC alignment layer instead of rubbed PI. Additionally, hydrogen plays an important role in LC alignment because of the difference in alignment properties between a-SiOx films and a-SiOx:H films. We investigate the mechanism of IB-treated inorganic alignment layers and suggest that LCs are aligned by chemical effects, such as van der Waals interaction, more than by physical effects, such as morphology effects, in the inorganic alignment layer irradiated by IB.