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PubMed1995

High-performance liquid chromatography of amino acids, peptides and proteins. CXXXIX. Impact of operating parameters in large-scale chromatography of proteins.

Large-scale chromatography has been playing an important role in downstream treatment processing in biotechnology. In order to improve the productivity, the throughput of the chromatographic equipment was often increased by increasing the flow-rate and/or by increasing the column sample loading. This paper reports the results of a study on the impact of these and other operating parameters in affinity and ion-exchange chromatographic columns when used for protein purification. A sectional model was developed to predict protein adsorption processes in a packed column. The formulations of this mathematical model are presented in the Appendix. The present study was carried out with computer simulation based on this model and using data obtained from laboratory-scale columns. This model can simulate both the adsorption and washing stages of the protein purification process for both porous and non-porous particles. The effects of changing operating parameters were simulated and contour plots were generated for the easy identification of these effects. It was shown that both flow-rate and column loading can have a considerable impact on the processing rate and the yield of the column. As for the column capacity utilization, the impact of changing flow-rate is not significant at column loading of less than 80% in the test case. It was suggest that the present investigation provides a systematic predictive strategy which will greatly reduce the need for expensive, labour-intensive and time-consuming experimental work during process scale-up.

Adsorption↗
PubMed1988

Method for an automatic analysis of the ECG.

A method is presented for an analysis of the ECG. Using cubic spline techniques we proceed first to a smoothing of the signal and then to the elimination of baseline drift. The properties of the calculated derivatives are used to establish criteria for the identification of the ECG waves and the measurement of their essential parameters. The complete procedure can be carried out by a computer, without human intervention. The results of this fully automatic procedure can be used directly as a means of classifying the ECG.

Algorithms↗
PubMed1990

Evaluation of Euler's angles with a least squares method for the study of lumbar spine motion.

To analyse intervertebral movements, methods with a high level of accuracy are required. Stereoradiographic methods have been used for a number of years to describe intervertebral movements, but their major problem is to identify the same anatomical landmarks, not only on the pair of radiographs used for three-dimensional reconstruction, but also on all the pairs used to analyse the displacements. To minimize the errors due to the incorrect identification of anatomical landmarks, a least squares method to resolve the parameters of Euler's angles was validated by means of measurements made on a spine obtained from a cadaver. The accuracy of this method varied between 0.69 degrees and 0.71 degrees in rotation and between 0.28 mm and 0.77 mm in translation. In addition, this method significantly corrected the position of the anatomical landmarks. Euler's angles, used with a least squares estimate, can provide accurate and precise results.

Aged↗
PubMed1994

Acquisition and processing of data for isotope-ratio-monitoring mass spectrometry.

Methods are described for continuous monitoring of signals required for precise analyses of 13C, 18O, and 15N in gas streams containing varying quantities of CO2 and N2. The quantitative resolution (i.e. maximum performance in the absence of random errors) of these methods is adequate for determination of isotope ratios with an uncertainty of one part in 10(5); the precision actually obtained is often better than one part in 10(4). This report describes data-processing operations including definition of beginning and ending points of chromatographic peaks and quantitation of background levels, allowance for effects of chromatographic separation of isotopically substituted species, integration of signals related to specific masses, correction for effects of mass discrimination, recognition of drifts in mass spectrometer performance, and calculation of isotopic delta values. Characteristics of a system allowing off-line revision of parameters used in data reduction are described and an algorithm for identification of background levels in complex chromatograms is outlined. Effects of imperfect chromatographic resolution are demonstrated and discussed and an approach to deconvolution of signals from coeluting substances described.

Alkanes↗
PubMed2005

A unified framework for unraveling the functional interaction structure of a biomolecular network based on stimulus-response experimental data.

We propose a unified framework for the identification of functional interaction structures of biomolecular networks in a way that leads to a new experimental design procedure. In developing our approach, we have built upon previous work. Thus we begin by pointing out some of the restrictions associated with existing structure identification methods and point out how these restrictions may be eased. In particular, existing methods use specific forms of experimental algebraic equations with which to identify the functional interaction structure of a biomolecular network. In our work, we employ an extended form of these experimental algebraic equations which, while retaining their merits, also overcome some of their disadvantages. Experimental data are required in order to estimate the coefficients of the experimental algebraic equation set associated with the structure identification task. However, experimentalists are rarely provided with guidance on which parameters to perturb, and to what extent, to perturb them. When a model of network dynamics is required then there is also the vexed question of sample rate and sample time selection to be resolved. Supplying some answers to these questions is the main motivation of this paper. The approach is based on stationary and/or temporal data obtained from parameter perturbations, and unifies the previous approaches of Kholodenko et al. (PNAS 99 (2002) 12841-12846) and Sontag et al. (Bioinformatics 20 (2004) 1877-1886). By way of demonstration, we apply our unified approach to a network model which cannot be properly identified by existing methods. Finally, we propose an experiment design methodology, which is not limited by the amount of parameter perturbations, and illustrate its use with an in numero example.

Computational Biology↗
PubMed2006

Quantification of intrinsic and reflexive properties during multijoint arm posture.

This study estimates intrinsic and reflexive properties of single- and two-joint muscles acting around the human shoulder, elbow and wrist joint during posture maintenance. External force disturbances were applied to the hand while subjects (n = 5) were instructed to minimize their hand displacement amplitude in a horizontal plane. To examine how the nervous system modifies intrinsic and reflexive muscle properties, we varied external damping, disturbance power and arm configuration. A new identification method is introduced to quantify a large set of model parameters describing intrinsic, activation and reflexive properties, the latter representing afferent feedback gains from muscle spindles and Golgi tendon organs. Consistent estimates were found for the gains of the different types of reflex pathways. The results showed that intrinsic visco-elasticity of shoulder muscles was minimal, whereas reflexive feedback was largest compared to the elbow and wrist joint. Intrinsic and reflexive properties of the two-joint shoulder-elbow muscles were larger than the two-joint elbow-wrist muscles. Contrasting to previous single-joint studies, the reflex gains did not vary with the experimental conditions. It is concluded that during redundant multijoint posture maintenance, the mechanical properties are efficiently controlled on the joint level and not on the endpoint level.

Adult↗
PubMed2005

Depression and cardiovascular disease: a reciprocal relationship.

Until relatively recently, depression has been considered a purely "mental" disorder and therefore in the natural domain of psychologists and psychiatrists. However, recent epidemiological studies have revealed that aging, physical and psychological stress, chronic pain, several metabolic disorders such as insulin resistance and established diabetes, alcoholism, inflammatory conditions, and vascular disorders such as arterial hypertension all may be associated with depression. The present review examines some of these depression-associated factors and the mechanisms by which they might give rise to vascular disorders such as atherosclerosis, microcirculation endothelial dysfunction, and interstitial disturbances leading to organ damage. A number of disorders involving the circulation can lead progressively and insidiously to large artery rigidity, remodeling of peripheral arteries, and alterations of the microcirculation of large blood vessels. Perturbations in vasa vasorum blood flow may contribute to atherogenesis, in addition to the influence of numerous cellular events involved in inflammation (tumor necrosis factor alpha, interleukin 1 beta, etc). Since Hans Selye first described the neuroendocrine cascade generated by experimentally induced stress half a century ago, phenomena such as the axonal release of neurotransmitters (including serotonin), accumulation of metabolites such as homocysteine, platelet-activating factor, and nitric oxide also have been implicated in the pathogenesis of depression. Moreover, vascular consequences of depression such as heart rate and pulse pressure variations may lead to endothelial dysfunction in critical microcirculation networks (cerebral, myocardial, and renal) and initiate physicochemical alterations in interstitial compartments adjacent to vital organs. The appropriate use of ambulatory monitoring of vascular parameters, such as heart rate and pulse pressure, and eventually, early identification of genetic and metabolic markers may prove helpful in the early detection of events preceding and predicting the clinical manifestations of depression.

Cardiovascular Diseases↗
PubMedDate not supplied

A new method to calculate the beat-to-beat instability of QT duration in drug-induced long QT in anesthetized dogs.

INTRODUCTION: Instability of QT duration is a marker to predict Torsade de Pointes (TdP) associated with both congenital and drug-induced long QT syndrome. We describe a new method for the quantification of instability of repolarization. METHODS: Female, adult beagle dogs anesthetized with a potent morphinomimetic were treated with either solvent (n=7) or dofetilide (n=7). Poincaré plots with QT(n) versus QT(n+1) were constructed to visualize the beat-to-beat variation in QT intervals from the lead II ECG. Short-term instability (STI), long-term instability (LTI) and total instability (TI) were quantified by calculating the distances of 30 consecutive data-points from the x and y-coordinate to the "centre of gravity" of the data cluster. Dofetilide at 0.0025 to 0.04 mg/kg i.v. (plasma concentrations of 4+/-0.6 to 41+/-2.7 ng/ml), dose-dependently prolonged QT and QTcV (at 0.04 mg/kg i.v.: QT: 280+/-ms versus 236+/-5 ms with solvent; p<0.05 and QTcV: 290+/-9 ms versus 252+/-4 ms with solvent; p<0.05). Concomitantly, the compound induced an increase in the instability parameters in a similar dose-dependent manner (at 0.04 mg/kg i.v.: TI: 6.8+/-0.9 ms versus 1.7+/-0.3 ms; p<0.05, LTI: 3.6+/-0.5 ms versus 1.0+/-0.2 ms; p<0.05 and STI: 4.2+/-0.6 ms versus 1.0+/-0.2 ms; p<0.05). The increases induced by dofetilide were associated with a high incidence of early afterdepolarizations (EADs) in the endocardial monophasic action potential (in 6 out of the 7 compound-treated animals versus 0 out of the 7 solvent animals; p<0.05). CONCLUSION: Quantification of beat-to-beat QT instability by our method clearly detects changes in short-term, long-term and total instability induced by dofetilide, already at pre-arrhythmic doses. Dofetilide administration to anesthetized dogs prolongs ventricular repolarization, concomitantly increases beat-to-beat QT instability and induces early after depolarizations (EADs). As such, the use of these parameters in this in vivo model shows clear potential for risk identification in cardiovascular safety assessment.

Anesthesia↗
PubMed2001

Effect of tissue Doppler on the accuracy of novice and expert interpreters of dobutamine echocardiography.

The subjective interpretation of dobutamine echocardiography (DBE) makes the accuracy of this technique dependent on the experience of the observer, and also poses problems of concordance between observers. Myocardial tissue Doppler velocity (MDV) may offer a quantitative technique for identification of coronary artery disease, but it is unclear whether this parameter could improve the results of less expert readers and in segments with low interobserver concordance. The aim of this study was to find whether MDV improved the accuracy of wall motion scoring in novice readers, experienced echocardiographers, and experts in stress echocardiography, and to identify the optimal means of integrating these tissue Doppler data in 77 patients who underwent DBE and angiography. New or worsening abnormalities were identified as ischemia and abnormalities seen at rest as scarring. Segmental MDV was measured independently and previously derived cutoffs were applied to categorize segments as normal or abnormal. Five strategies were used to combine MDV and wall motion score, and the results of each reader using each strategy were compared with quantitative coronary angiography. The accuracy of wall motion scoring by novice (68 +/- 3%) and experienced echocardiographers (71 +/- 3%) was less than experts in stress echocardiography (88 +/- 3%, p <0.001). Various strategies for integration with MDV significantly improved the accuracy of wall motion scoring by novices from 75 +/- 2% to 77 +/- 5% (p <0.01). Among the experienced group, accuracy improved from 74 +/- 2% to 77 +/- 5% (p <0.05), but in the experts, no improvement was seen from their baseline accuracy. Integration with MDV also improved discordance related to the basal segments. Thus, use of MDV in all segments or MDV in all segments with wall motion scoring in the apex offers an improvement in sensitivity and accuracy with minimal compromise in specificity.

Aged↗
PubMed2003

Differential apolipoprotein(a) isoform expression in heterozygosity is an independent contributor to lipoprotein(a) levels variability.

BACKGROUND AND METHODS: Lipoprotein(a) [Lp(a)] levels represent an independent risk factor for cardio- and cerebrovascular diseases. Since lipoprotein(a) levels show a wide variability even in subjects with similar apolipoprotein(a) isoforms, we investigated the contribution of apolipoprotein(a) heterozygosity to lipoprotein(a) variance. Lipoprotein(a) levels, apolipoprotein(a) isoforms identification and expression, and the correlation with other lipo-apolipoprotein parameters have been investigated in 628 subjects >18 years of age. RESULTS: In our study, 246 subjects were found heterozygous for apolipoprotein(a) isoforms. Lipoprotein(a) levels were higher in females. About 40% of the subjects expressed the larger isoform more intensely than the dominant isoform. Lipoprotein(a) was correlated with apolipoprotein(a) dominant isoform size, HDL-cholesterol and smaller apolipoprotein(a) isoform expression rate. Lipoprotein(a) was independently correlated with the smaller apolipoprotein(a) isoform, with its expression rate and with LDL-cholesterol. The inclusion of the smaller apolipoprotein(a) expression rate in a multiple regression model explained at least an additional 4% of the lipoprotein(a) variance after correction for apolipoprotein(a) size. CONCLUSIONS: The smaller isoforms are not always effectively dominant in heterozygosis since 40% of the subjects expressed more the larger isoform. The individual variability of apolipoprotein(a) isoform expression in heterozygosis could explain part of the lipoprotein(a) levels variability.

Adult↗
PubMed2002

Gas chromatographic determination of 2-hydroxy-4-methoxybenzophenone and octyldimethyl-p-aminobenzoic acid sunscreen agents in swimming pool and bathing waters by solid-phase microextraction.

A method has been developed for the trace determination of two sunscreen constituents (2-hydroxy-4-methoxybenzophenone and octyldimethyl-p-aminobenzoic acid) in water samples, which are commonly used in commercial formulations. The method employs solid-phase microextraction (SPME) and gas chromatography with flame ionization and mass spectrometric detection. The technique was developed with headspace and direct sampling in order to demonstrate the applicability of these SPME extraction modes for the identification of these two UV absorbing compounds in waters. The main parameters affecting the SPME process, such as desorption time, extraction time profile, salt additives, pH, and temperature, were investigated. The poly(dimethylsiloxane) 100-microm and polyacrylate 85-microm fiber coatings were found to be the most efficient for the extraction of these compounds from aqueous matrices. Linear calibration curves in the wide range of 10-500 microg/l were obtained for both compounds yielding typical RSD values of 5-9% for both extraction modes. The recoveries were relatively high, 82-98%, with quantitation limits below 1 microg/l. A comparison between the proposed methods and the conventional multiresidue solid-phase extraction revealed that the proposed technique(s) can be reliably used for sunscreen residue measurement in water samples with satisfactory results.

4-Aminobenzoic Acid↗
PubMed2002

XMAP215: a key component of the dynamic microtubule cytoskeleton.

Microtubules are essential for various cellular processes including cell division and intracellular organization. Their function depends on their ability to rearrange their distribution at different times and places. Microtubules are dynamic polymers and their behaviour is described as dynamic instability. Rearrangement of the microtubule cytoskeleton is made possible by proteins that modulate the parameters of dynamic instability. Studies using Xenopus egg extracts led to identification of a microtubule-associated protein called XMAP215 as a major regulator of physiological microtubule dynamics. XMAP215 belongs to an evolutionarily conserved protein family present in organisms ranging from yeast to mammals. Together with members of the Kin I family of kinesins, XMAP215 and its orthologues form an essential circuit for generating dynamic microtubules in vivo.

Animals↗
PubMed1998

In vitro culture growth of erythroid progenitors and serum erythropoietin assay in the differential diagnosis of polycythaemia.

BACKGROUND: We assessed the in vitro culture growth of erythroid progenitors [burst forming unit-erythroid (BFU-E)] and serum erythropoietin (EPO) levels in different groups of polycythaemia to determine the discriminative power in differential diagnosis of polycythaemia. METHODS: We used the methylcellulose culture technique to study the growth of endogenous erythroid colonies (EECs) and EPO-dependent BFU-E from bone marrow (BM) and/or peripheral blood (PB) cells from 40 patients with polycythaemia vera (PV), 13 with secondary polycythaemia (SP), 19 with pure erythrocytosis (PE), five with PE and PV evolution later (PE-PV), and 12 with relative polycythaemia (RP). The serum EPO levels were measured by radioimmunoassay before treatment in 47 patients, 23 SP patients, 19 PE patients, five PE-PV patients and 16 RP patients, as well as after treatment in 38 PV patients, five PE-PV patients and 12 PE patients. RESULTS: The results of the erythroid progenitor culture assay showed that the numbers of EPO-dependent BFU-E in BM did not differ significantly among groups. The PB BFU-E were significantly higher in PV than in SP or PE, and no statistical difference were found among patients with SP, PE and RP. There was a correlation between BM BFU-E and PB BFU-E in the individual PV and PE patients. EECs were present in all BM and PB cultures of untreated and phlebotomy-treated PV and PE-PV patients, but were absent in 6 of 17 PV patients who had received cytotoxic therapy. EECs were not found in SP, PE and RP. PB could substitute for BM in the EEC or the BFU-E assay. Both pretreatment and post-treatment serum EPO levels of PV and PE-PV were similar, which were significantly lower than SP, PE or RP. The serum EPO levels in treated PV or PE-PV patients who had normal haematocrit values were not significantly different from those in untreated patients. In contrast, the phlebotomy-treated PE patients had significantly higher serum EPO values than untreated PE patients. In the differentiation between PV and PE, the sensitivity, specificity, positive predictive value and negative predictive value of post-treatment serum EPO levels at a cut-off level of < or = 9 UL-1 were 74%, 92% and 52% respectively. The discriminative power of post-phlebotomy serum EPO levels was even higher with a positive predictive value of 80% and negative predictive value of 92% for the prediction of PV evolution in patients with pure erythrocytosis of unknown origin. CONCLUSION: The present study showed that apart from EEC assay, the post-phlebotomy serum EPO level was a sensitive and specific parameter in the differential diagnosis of polycythaemia, in particular for the identification of PV among patients with unclassifiable polycythaemia.

Adult↗
PubMedDate not supplied

Improving blood transfusion practice: role of a computerized hospital information system.

The recent focus on medical risk and financial cost has prompted a need for better guidelines for prescribing the transfusion of blood components. In 1987, to respond to the issues of quality transfusion practice and accurate evaluation, LDS Hospital (Salt Lake City, UT) began using a computerized, knowledge-based blood-ordering system. Each transfusion request was reviewed and flagged by the computer when it did not meet the criteria established by the medical staff. The study reviewed the use of red cells, platelets, and fresh-frozen plasma in 13,082 transfusion orders for 5847 consecutive patients from July 1, 1988, through June 30, 1989. The evaluation assessed, first, the adherence of physicians to computerized criteria and, second, their adherence to the quality of transfusion practice. A high percentage of the blood units ordered met the established criteria: 91.2 percent for the red cell transfusions, 72.9 percent for platelets, and 81.7 percent for fresh-frozen plasma. From the July 1, 1987, implementation date through June 1989, the mean hematocrit of persons being transfused dropped from 28.6 to 27.7 percent (0.29 = 0.28) (p less than 0.005) and the number of orders requiring review by the quality assurance department dropped from 100 to 14 percent; moreover, there was a true-exception rate of only 0.37 percent. The use of the computer system effected the implementation of the following measures: 1) identification of the indications and establishment of clear clinical and biologic parameters for every transfusion, and 2) measurement and improvement of institutional transfusion practice. These results demonstrated the efficacy of a computerized hospital information system in implementing continuous quality improvement for transfusion practice.(ABSTRACT TRUNCATED AT 250 WORDS)

Blood Transfusion↗
PubMed1990

[Spectrum analysis of Doppler signals].

Doppler signal spectrum analysis contains useful haemodynamic information. Several parameters of the spectrum can be documented in numerics. Random interaction of the reflectors, the size of the ultrasound sample volume and the procedure of signal analysis influence the results and hence may cause misinterpretation of the data selected. Essential mechanisms influencing the clinician's Doppler-spectrum-analysis are discussed on the basis of a series of 59 angiographically and sonographically examined carotid arteries as well as in the light of theoretical considerations and a review of the literature. Peak frequency linked with a battery of spectrum parameters accuracy are useful to differentiate various degrees of lumen narrowing. Identification or exclusion of minor plaques cannot be achieved with sufficient sensitivity and specificity.

Carotid Arteries↗
PubMed2000

Thermal lesions produced by CO2 laser beams: new findings to improve the quality of minimally invasive and transmyocardial laser revascularization protocols.

OBJECTIVE: The objective of this study was to investigate the possible existence of a set of critical combinations among medical CO2 laser device set-ups and to compare the resigns of diameter and depth of irradiated tissue. These data are useful to the surgeon to identify a general operative protocol that allows both to forecast the beam behavior on a large variety of operative conditions accurately and to identify the related safety margins. Two methods have been addressed: the more traditional free-air beam delivery to the tissue and the more modern requirements of the minimally invasive surgery concepts, which use fiberoptic-based delivery systems for the CO2 laser beam. BACKGROUND DATA: In the past many articles have been written about the interaction between laser beams and biological media. However, the CO2 laser beam at 10.6 microm has always challenged research institutions and manufacturers to find the ideal combinations between a suitable fiberoptic-based delivery system concept and the injury threshold conditions recommended for minimally invasive surgery (MIS) and transmyocardial laser revascularization (TMLR) applications. One of the main challenges is to deliver the radiation at 10.6 microm without serious damage to the fiberoptic-based scalpel and the irradiated tissue by the burn of the fiber in use. METHODS: Five rabbits weighing 3 to 3.5 kg were sacrificed and 60 samples of trachea, myocardium, aorta, and esophagus were immediately excised, trimmed free of the adherent connective tissue, and irradiated in the intima portion of the wall. A commercial TEM medical CO2 laser was coupled to a silver halide fiber (0.9 mm in diameter) and subsequently to regular focusing heads (2.5-inch and 5-inch focal length) for pulsed laser beam delivery. The parameters chosen were: 33, 50, 65, and 100 mJ per pulse, 10 and 20 ms pulse width, delivered in two sets of experiments, one with all the pulsed beam frequencies below 5 Hz, the other between 15 Hz and 20 Hz. The same tests were conducted on 10 blocks of 3 different plastic types to simulate in one single procedure the laser radiation in responses to both hard, low-water content tissues such as bone and of common plastic compounds (such as polymethylmethacrylates [PMMA]) routinely used in orthopedic surgery. An optical microscope was used to measure all the lesions (diameter and depth in millimeters) in all the samples and to identify the smallest and the largest one against which similar thermal injuries found on the other media were compared. RESULTS: This study demonstrates that for power densities between about 520 and 790 W/cm2 per pulse achieved with the silver halide fiber generated a minimal lesion on the myocardium and aortic tissues. This can be used as reference threshold for MIS and TMLR. The minimal injury threshold on PMMA has been reached at 393 W/cm2 per pulse at 1 Hz. This approached the conditions of a pulsed beam delivered in air on the same medium via a focal spot of an 8.7 inch focal. Surprisingly, all the treated media show lesions that follow similar patterns within a well-defined and limited range of both diameter and depth. This effect was obtained by using power densities ranging from 393 to 6310 W/cm2 per pulse regardless of all the other parameters, including power delivery method, the type of irradiated tissue and the frequency between 0 and 20 Hz. Only the combination power density-type of tissue appears to be decisive. The geometrical convergence of the diameter shows a much smoother pattern than the one of the depth, due to two different irradiation modalities. CONCLUSIONS: The selection of the CO2 laser beam parameters and the irradiated media reported in this article have allowed identification of a critical set of ablative conditions to be further used in the operating room.

Animals↗
PubMed1985

Widely disseminated Cunninghamella mucormycosis in an adult renal transplant patient: case report and review of the literature.

A case of widely disseminated mucormycosis involving Cunninghamella bertholletiae is reported. This represents the first report of Cunninghamella infection in a transplant patient and, to our knowledge, only the eighth reported case of human infection by this saprophytic fungus. The clinical course was similar to most of the previously reported cases in that the patient was immunocompromised prior to the infection and the diagnosis was made too late for appropriate therapeutic intervention. The current case is unique in that it involved a renal allograft recipient; that the major clinical signs and symptoms mimicked myocardial infarction; and that there was more widespread dissemination than in earlier cases. The histologic and laboratory identification of the fungus are presented and correlated with the clinical parameters (signs, symptoms, and therapy) of this case as well as the cases previously reported in the literature.

Adult↗
PubMed1998

Bayesian adaptive sequence alignment algorithms.

The selection of a scoring matrix and gap penalty parameters continues to be an important problem in sequence alignment. We describe here an algorithm, the 'Bayes block aligner, which bypasses this requirement. Instead of requiring a fixed set of parameter settings, this algorithm returns the Bayesian posterior probability for the number of gaps and for the scoring matrices in any series of interest. Furthermore, instead of returning the single best alignment for the chosen parameter settings, this algorithm returns the posterior distribution of all alignments considering the full range of gapping and scoring matrices selected, weighing each in proportion to its probability based on the data. We compared the Bayes aligner with the popular Smith-Waterman algorithm with parameter settings from the literature which had been optimized for the identification of structural neighbors, and found that the Bayes aligner correctly identified more structural neighbors. In a detailed examination of the alignment of a pair of kinase and a pair of GTPase sequences, we illustrate the algorithm's potential to identify subsequences that are conserved to different degrees. In addition, this example shows that the Bayes aligner returns an alignment-free assessment of the distance between a pair of sequences.

Adenylate Kinase↗