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PubMed1988

The V gamma locus of the human T cell receptor gamma gene. Repertoire polymorphism of the first variable gene segment subgroup.

Southern blot analysis using a genomic probe of the human TCR-gamma chain first variable gene subgroup (V gamma I) was performed on DNA samples from both parents of 36 healthy Caucasian families. Two types of polymorphisms were found in these 72 unrelated DNA samples: three repertoire polymorphisms and two restriction fragment length polymorphisms (RFLP). In all cases, Mendelian inheritance of these polymorphisms was demonstrated. The most frequent repertoire polymorphism consists in the lack of the V gamma 4 and V gamma 5 segments. In 16% of chromosomes, the Eco RI and Taq I restriction fragments corresponding to V gamma 4 and V gamma 5 were lacking, with no additional bands. In these cases, a decrease of 10 kb was observed in the Bam HI fragment containing all V gamma I segments as compared with samples containing V gamma 4-V gamma 5 segments. To better understand this polymorphism, which takes place in a previously incompletely defined region, the central part of the V gamma I region, including the polymorphic V gamma 4-V gamma 5 segments, was cloned. This allowed us to localize precisely the V gamma 5 segment and thus complete the description of the V gamma I region. A striking homology of DNA and deduced amino acid sequences is present between V gamma 2 and V gamma 4 and between V gamma 3 and V gamma 5, much higher than that observed between V gamma 2 and V gamma 3 and between V gamma 4 and V gamma 5. The differences in nucleotide sequence occur mainly in the intron and three hypervariable regions. These results strongly suggest a gene duplication relationship between the segments V gamma 2-V gamma 3 and the segments V gamma 4-V gamma 5. The most frequent RFLP documented in this study is due to the combined absence of the Eco RI and the Taq I sites located in the noncoding region between V gamma 3 and V gamma 4. The haplotypic frequence of this RFLP is 6.9% of the general population. As the gamma/delta receptor may play an important role in immunological response, the biological relevance of the high degree of polymorphism occurring in the V gamma I region, as well as its possible association with some immune disturbances, should be further explored.

Amino Acid Sequence↗
PubMed2002

The use of mixed-integer programming for inverse treatment planning with pre-defined field segments.

Complex intensity patterns generated by traditional beamlet-based inverse treatment plans are often very difficult to deliver. In the approach presented in this work the intensity maps are controlled by pre-defining field segments to be used for dose optimization. A set of simple rules was used to define a pool of allowable delivery segments and the mixed-integer programming (MIP) method was used to optimize segment weights. The optimization problem was formulated by combining real variables describing segment, weights with a set of binary variables, used to enumerate voxels in targets and critical structures. The MIP method was compared to the previously used Cimmino projection algorithm. The field segmentation approach was compared to an inverse planning system with a traditional beamlet-based beam intensity optimization. In four complex cases of oropharyngeal cancer the segmental inverse planning produced treatment plans, which competed with traditional beamlet-based IMRT plans. The mixed-integer programming provided mechanism for imposition of dose-volume constraints and allowed for identification of the optimal solution for feasible problems. Additional advantages of the segmental technique presented here are: simplified dosimetry, quality assurance and treatment delivery.

Algorithms↗
PubMed2002

Fuzzy clustering-based segmented attenuation correction in whole-body PET imaging.

Segmented attenuation correction is now a widely accepted technique to reduce noise propagation from transmission scanning in positron emission tomography (PET). In this paper, we present a new method for segmenting transmission images in whole-body scanning. This reduces the noise in the correction maps while still correcting for differing attenuation coefficients of specific tissues. Based on the fuzzy C-means (FCM) algorithm, the method segments the PET transmission images into a given number of clusters to extract specific areas of differing attenuation such as air, the lungs and soft tissue, preceded by a median filtering procedure. The reconstructed transmission image voxels are, therefore, segmented into populations of uniform attenuation based on knowledge of the human anatomy. The clustering procedure starts with an overspecified number of clusters followed by a merging process to group clusters with similar properties (redundant clusters) and removal of some undesired substructures using anatomical knowledge. The method is unsupervised, adaptive and allows the classification of both pre- or post-injection transmission images obtained using either coincident 68Ge or single-photon 137Cs sources into main tissue components in terms of attenuation coefficients. A high-quality transmission image of the scanner bed is obtained from a high statistics scan and added to the transmission image. The segmented transmission images are then forward projected to generate attenuation correction factors to be used for the reconstruction of the corresponding emission scan. The technique has been tested on a chest phantom simulating the lungs, heart cavity and the spine, the Rando-Alderson phantom, and whole-body clinical PET studies showing a remarkable improvement in image quality, a clear reduction of noise propagation from transmission into emission data allowing for reduction of transmission scan duration. There was very good correlation (R2 = 0.96) between maximum standardized uptake values (SUVs) in lung nodules measured on images reconstructed with measured and segmented attenuation correction with a statistically significant decrease in SUV (17.03% +/- 8.4%, P < 0.01) on the latter images, whereas no proof of statistically significant differences on the average SUVs was observed. Finally, the potential of the FCM algorithm as a segmentation method and its limitations as well as other prospective applications of the technique are discussed.

Algorithms↗
PubMed2002

Comparison of segmental and global bioimpedance spectroscopy errors using generalizability theory.

The generalizability theory, an expansion of classic true-score reliability theory, was used to investigate the generalizability of observed segmental extracellular fluid (ECF) and intracellular fluid (ICF) distribution measurements. The test instrument was a Xitron Hydra ECF/ICF bioimpedance analysis system model 4200, Xitron Technologies, San Diego, CA. Fifty American healthy men (17-72 years) and 50 American healthy women (17-76 years) volunteered as participants. Xitron continuous segmental ECF-ICF procedures for testing leg segmental data were followed for testing participants in both the standing erect and lying supine postures. A two-facet, person-by-trial, completely crossed design was used. All facets were treated as random. During a one-day session each subject was tested involving 20 trials for the standing erect posture and 20 trials for the lying supine posture. Data on each fluid measurement, each body posture and each sex group were independently analysed. The analyses revealed that the trial factor accounted for less than 0.2% of the total variance for ECF and ICF scores. ECF and ICF generalizability coefficients for the segmental method were 0.99 or greater. In comparing ECF segmental to ECF global, results showed generalizability coefficients were similar. However, ICF segmental coefficients were larger than the coefficients produced by the global method. In conclusion, the segmental method appeared more reliable than the global method, under the conditions of this study.

Adolescent↗
PubMed2005

Current density distributions, field distributions and impedance analysis of segmented deep brain stimulation electrodes.

Deep brain stimulation (DBS) electrodes are designed to stimulate specific areas of the brain. The most widely used DBS electrode has a linear array of 4 cylindrical contacts that can be selectively turned on depending on the placement of the electrode and the specific area of the brain to be stimulated. The efficacy of DBS therapy can be improved by localizing the current delivery into specific populations of neurons and by increasing the power efficiency through a suitable choice of electrode geometrical characteristics. We investigated segmented electrode designs created by sectioning each cylindrical contact into multiple rings. Prototypes of these designs, made with different materials and larger dimensions than those of clinical DBS electrodes, were evaluated in vitro and in simulation. A finite element model was developed to study the effects of varying the electrode characteristics on the current density and field distributions in an idealized electrolytic medium and in vitro experiments were conducted to measure the electrode impedance. The current density over the electrode surface increased towards the edges of the electrode, and multiple edges increased the non-uniformity of the current density profile. The edge effects were more pronounced over the end segments than over the central segments. Segmented electrodes generated larger magnitudes of the second spatial difference of the extracellular potentials, and thus required lower stimulation intensities to achieve the same level of neuronal activation as solid electrodes. For a fixed electrode conductive area, increasing the number of segments (edges) decreased the impedance compared to a single solid electrode, because the average current density over the segments increased. Edge effects played a critical role in determining the current density distributions, neuronal excitation patterns, and impedance of cylindrical electrodes, and segmented electrodes provide a means to increase the efficiency of DBS.

Animals↗
PubMed2003

Fast identification and statistical evaluation of segmental homologies in comparative maps.

MOTIVATION: Chromosomal segments that share common ancestry, either through genomic duplication or species divergence, are said to be segmental homologs of one another. Their identification allows researchers to leverage knowledge of model organisms for use in other systems and is of value for studies of genome evolution. However, identification and statistical evaluation of segmental homologies can be a challenge when the segments are highly diverged. RESULTS: We describe a flexible dynamic programming algorithm for the identification of segments having multiple homologous features. We model the probability of observing putative segmental homologies by chance and incorporate our findings into the parameterization of the algorithm and the statistical evaluation of its output. Combined, these findings allow segmental homologies to be identified in comparisons within and between genomic maps in a rigorous, rapid, and automated fashion.

Algorithms↗
PubMed2005

Segmentation of cDNA microarray spots using markov random field modeling.

MOTIVATION: Spot segmentation is a critical step in microarray gene expression data analysis. Therefore, the performance of segmentation may substantially affect the results of subsequent stages of the analysis, such as the detection of differentially expressed genes. Several methods have been developed to segment microarray spots from the surrounding background. In this study, we have proposed a new approach based on Markov random field (MRF) modeling and tested its performance on simulated and real microarray images against a widely used segmentation method based on Mann-Whitney test adopted by QuantArray software (Boston, MA). Spot addressing was performed using QuantArray. We have also devised a simulation method to generate microarray images with realistic features. Such images can be used as gold standards for the purposes of testing and comparing different segmentation methods, and optimizing segmentation parameters. RESULTS: Experiments on simulated and 14 actual microarray image sets show that the proposed MRF-based segmentation method can detect spot areas and estimate spot intensities with higher accuracy.

Algorithms↗
PubMed1988

A non-linear elastic model of contraction of ischaemic segments.

Previous studies have characterised the motion of the myocardium using a linear time varying elastance model, ie, they have sought to characterise the relationship between left ventricular volume and internal pressure as linear, but with time varying slopes over the cardiac cycle. However, the motion of myocardium during regional ischaemia has not been characterized by such models. Studies of totally ischaemic tissue and of myocardium in diastole have characterised the relationship between tension or stress and segment length as exponential. It is the purpose of this study to present a new model in which myocardial contraction is expressed as an exponential, but time varying elastic relationship. In this model tension, T, is related to segment length according to the formula T = e alpha(t)L + beta, where alpha(t) rises with systole and falls in diastole. This model was applied to the motion of hypokinetic segments noted in a series of conscious dogs studied for other purposes. Hypokinetic segments display early systolic bulging, decreased systolic shortening, and early diastolic recoil. These particular types of segment motion are naturally predicted by this model. Furthermore, the motion of myocardial segments as they become increasingly ischaemic may be predicted, including a gradual shift to the right and narrowing of the tension-length loop. alpha was noted to be independent of loading change, and thus may be viewed as an index of contractility. This model thus predicts the pattern of motion of hypokinetic segments and provides new insight into myocardial contractility.

Animals↗
PubMed1988

Segmental volume distensibility of the canine thoracic aorta in vivo.

Segments of the canine ascending aorta, upper descending thoracic aorta, and middle descending thoracic aorta were instrumented with ultrasonic dimension gauges and a cathetertip manometer simultaneously to measure changes in segment diameter, length, and intravascular pressure. Volume distensibility (EV) was calculated as the sum of circumferential extensibility (EC), longitudinal extensibility (EL), and high order extensibilities (EK) for each segment. The EC and EL were linear expressions that represented percentage volume changes per mmHg pulse pressure due to circumferential and longitudinal dimensional changes. The high order extensibilities (second and third order) accounted for the percentage volume changes per mmHg pulse pressure due to the interactions between circumferential and longitudinal dimensional changes. Mean(SEM) EV values from six dogs were 1.62(0.31), 0.84(0.08), and 0.62(0.08)% delta V/mmHg delta P for the ascending aorta, upper descending thoracic aorta, and middle descending thoracic aorta segments respectively. The EV, EL, and EK of the ascending aorta segment were significantly greater than those of the upper descending thoracic aorta and middle descending thoracic aorta segments, whereas EC was significantly less in the ascending aorta than in both the upper descending thoracic aorta and middle descending thoracic aorta segments. It is concluded that there are regional differences in aortic distensibility and its components in vivo. Longitudinal wall motion is an important determinant of these aortic mechanical properties.

Animals↗
PubMed1993

Dipyridamole echocardiography evaluation of acute inferior myocardial infarction with concomitant anterior ST segment depression.

The significance of anterior ST segment depression in inferior acute myocardial infarction (AMI) remains controversial. The aim of this study was to relate precordial ST segment depression to the topography of residual myocardial ischaemia, with myocardial mapping of the asynergic area and coronary anatomy. Twenty-five patients with first inferior AMI (15 patients with anterior ST segment depression: group A and 10 patients without anterior ST segment shift: group B), all underwent: (1) electrocardiographic evaluation on admission to the Coronary Care Unit and at 24 h intervals thereafter; (2) 2D-echocardiographic study within 3 h of CCU admission; (3) dipyridamole echocardiographic test (DET) (doses of dipyridamole up to 0.84 mg.kg-1 i.v. over 10 min) 4 days after AMI; (4) coronary arteriography within 14 days from AMI. To assess regional left ventricular wall motion, a 16 segment model was used and a wall motion score index (WMSI) was derived. The results of DET were correlated to the anatomy of the infarct-related vessel. Compared to group B, group A patients showed a significantly greater maximal ST segment elevation in inferior limb leads (lead III: 3.9 +/- 1.9 mm vs 2.2 +/- 1.1 mm, P < 0.05; aVF: 3.5 +/- 1.3 mm vs 1.7 +/- 0.8 mm, P < 0.001). Group A patients showed greater WMSI (1.35 +/- 0.22 vs 1.17 +/- 0.12, P < 0.05), with more frequent postero-lateral wall involvement (72% vs 20%, P < 0.05). No patient of either group showed asynergy of the anterior, anterolateral or anteroseptal segments. No differences in the distribution of coronary artery disease were observed.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗
PubMed2005

Topogenic properties of transmembrane segments of Arabidopsis thaliana NHX1 reveal a common topology model of the Na+/H+ exchanger family.

The membrane topology of the Arabidopsis thaliana Na(+)/H(+) exchanger isoform 1 (AtNHX1) was investigated by examining the topogenic function of transmembrane (TM) segments using a cell-free system. Even though the signal peptide found in the human Na(+)/H(+) exchanger (NHE) family is missing, the N-terminal hydrophobic segment was efficiently inserted into the membrane and had an N-terminus lumen topology depending on the next TM segment. The two N-terminal TM segments had the same topology as those of TM2 and TM3 of human NHE1. In contrast, TM2 and TM3 of human NHE1 did not acquire the correct topology when the signal peptide (denoted as TM1) was deleted. Furthermore, there were three hydrophobic segments with the same topogenic properties as the TM9-H10-TM10 segments of human NHE1, which has one lumenal loop (H10) and two flanking TM segments (TM9 and TM10). These data indicate that the plant NHX isoforms can form the common membrane topology proposed for the human NHE family, even though it does not have a signal peptide.

Amino Acid Sequence↗
PubMed2003

A compositional segmentation of the human mitochondrial genome is related to heterogeneities in the guanine mutation rate.

We applied a hidden Markov model segmentation method to the human mitochondrial genome to identify patterns in the sequence, to compare these patterns to the gene structure of mtDNA and to see whether these patterns reveal additional characteristics important for our understanding of genome evolution, structure and function. Our analysis identified three segmentation categories based upon the sequence transition probabilities. Category 2 segments corresponded to the tRNA and rRNA genes, with a greater strand-symmetry in these segments. Category 1 and 3 segments covered the protein- coding genes and almost all of the non-coding D-loop. Compared to category 1, the mtDNA segments assigned to category 3 had much lower guanine abundance. A comparison to two independent databases of mitochondrial mutations and polymorphisms showed that the high substitution rate of guanine in human mtDNA is largest in the category 3 segments. Analysis of synonymous mutations showed the same pattern. This suggests that this heterogeneity in the mutation rate is partly independent of respiratory chain function and is a direct property of the genome sequence itself. This has important implications for our understanding of mtDNA evolution and its use as a 'molecular clock' to determine the rate of population and species divergence.

Algorithms↗
PubMed1996

Hypersensitivity of human coronary segments to ergonovine 6 months after injury by coronary angioplasty: a quantitative angiographic study in consecutive patients undergoing single-vessel angioplasty.

OBJECTIVE: Multiple studies have been designed to analyse restenosis angiographically but few have studied the vasoreactivity of coronary segments subjected to angioplasty a few months before. In the present study we analysed, with use of quantitative angiography, the vasoreactivity of previously dilated segments to graded doses of ergonovine and of isosorbide dinitrate. PATIENTS: Fifty consecutive patients undergoing follow-up angiography 6 months after a single coronary angioplasty procedure were studied. RESULTS: The vasoconstrictor response at dilated segments (-19.3 +/- 3.0%) was significantly greater than at control proximal and distal sites in dilated (-7.3 +/- 1.1%, -11.0 +/- 2.9%) and non-dilated (-9.1 +/- 1.3%, -8.3 +/- 2.2%) vessels for the lowest dose of ergonovine (100 micrograms). The constrictor response to 100 micrograms ergonovine (-20.2 +/- 5.3%) at restenosed segments (> 50% stenosis, n = 18) was similar to that (-18.8 +/- 3.8%) at non-restenosed sites (n = 32). In contrast, the degree of constrictor response was similar in all segments including dilated segments for the highest dose of ergonovine used. All segments dilated significantly after intracoronary injection of isosorbide dinitrate. CONCLUSION: Our results demonstrate hypersensitivity of the dilated site to ergonovine 6 months after angioplasty at both restenosed and non-restenosed sites. This response may reflect partial dysfunction of endothelium that has regenerated after injury or hypersensitivity of vascular smooth muscle cells at the site of arterial injury.

Aged↗
PubMed1989

Increased mortality in men with ST segment depression during 24 h ambulatory long-term ECG recording. Results from prospective population study 'Men born in 1914', from Malmö, Sweden.

'Men born in 1914', from Malmö, Sweden, is a cohort study of the morbidity and mortality of cardiovascular diseases among 68-year-old men in an urban population. Ambulatory long-term ECG recording was part of the health examination that these men were invited to undergo in 1982. Five hundred attended (80.5%) of the 621 invited. Ninety-eight of the 394 men in whom the ECG recording was technically satisfactory had at least one episode with horizontal or downsloping ST segment depression greater than or equal to 0.1 mV. The median total duration of ST segment depression was 135 min. 90% of these episodes were not preceeded by any increase in heart rate. In only eight of the 47 men who reported an occurrence of chest symptoms during the recording period did ST segment depression and chest symptoms occur simultaneously. 43 months after the health examination, 33 (8.4%) men had died. The mortality in men without ST segment depression and without any history of coronary heart disease was 6.5%. The incidence of fatal and non-fatal myocardial infarction in men without ST depression greater than or equal to 0.1 mV and without a history of IHD was 2.3%. Men with ST depression greater than or equal to 0.1 mV in comparison with this group had a 4.4 times greater relative risk. The risk in men with both ST segment depression greater than or equal to 0.1 mV and history of coronary heart disease was 16.0 times greater. This study shows that asymptomatic ST segment depression is a frequent finding in elderly men. The occurrence of asymptomatic ST segment depression is associated with an increased cardiovascular mortality. This increased mortality is independent of a history compatible with angina pectoris or previous myocardial infarction.

Aged↗
PubMed1995

ST segment depression in lateral limb leads in inferior wall acute myocardial infarction. Implications regarding the culprit artery and the site of obstruction.

We examined whether the pattern of ST segment depression in lateral leads (I, aVL, V5, V6) in the initial electrocardiogram of patients (n = 88) with inferior wall acute myocardial infarction (ST segment elevation of > or = mm in > or = 2 inferior leads) correlates with the site of obstruction, as determined angiographically during acute hospitalization. Of the 62 patients in which the culprit artery could be determined unequivocally, in 46 the culprit artery was the right coronary artery (20 proximal to the first right ventricular branch and 26 distal), and in 16 the left circumflex coronary artery (seven proximal to the first marginal branch or involving a high first marginal branch, and nine with distal obstruction). Significant ST segment depression (ST < or = 1 mm) in leads I and aVL was more common in right coronary artery obstruction (P < 0.05 and P < 0.0001, respectively). The absence of significant ST segment depression in lead aVL was most common in proximal circumflex obstruction (P < 0.0001), with a similar trend for lead I (P < 0.11). ST segment depression patterns in leads V5 and V6 were not indicative of the infarct-related artery or the site of obstruction. Thus, significant ST segment depression in leads I and aVL indicates right coronary artery-associated inferior wall acute myocardial infarction with a sensitivity of 70% and 100%, and a specificity of 63% and 38%, respectively, whereas the lack of ST segment depression in these leads indicates proximal circumflex obstruction with a sensitivity of 71% and 86%, and a specificity of 65% and 100%, respectively.

Coronary Angiography↗
PubMed1995

Further elevation of the ST segment during the first hour of thrombolysis. A possible early marker of reperfusion.

OBJECTIVES: To evaluate the clinical implications of early electrocardiographic changes during thrombolysis in a randomized study in patients with an acute myocardial infarction. BACKGROUND: Re-elevation of a rapidly resolving ST segment during thrombolysis is currently interpreted as a sign of re-occlusion, but a further elevation at very early stages of lytic therapy may not necessarily have the same implications. METHODS: In 214 patients with a first transmural acute myocardial infarction of < or = 4 h randomized to fibrinolytic (streptokinase group, n: 110) vs non fibrinolytic medical therapy (control group, n: 104), a standard 12 lead ECG was continuously recorded during the first 60 min and at 2, 4, 10, 16 and 24 h. Serial enzymes were measured during 72 h, and in 156 patients (73%) a coronary angiogram was performed at 10-15 days. RESULTS: Within the first 20-40 min there was an additional ST segment elevation in 50 patients (45%) from the streptokinase group and in 19 from control group (18%) (P < 0.0001) but the increment was greater in the streptokinase group (1.2 +/- 1.4 vs 0.3 +/- 1.4 mm, P < 0.0001). In the streptokinase group, the interval from onset of pain to peak creatine kinase MB was shorter in patients with additional ST segment elevation than in those without it (699 +/- 193 vs 856 +/- 299 min, P < 0.01). Moreover, in-hospital mortality tended to be lower in patients whose ST segment was elevated than in those without such elevation (2150, 4%, vs 6160, 10%). Incidence of recanalization was high but comparable in these two subsets. In recanalized patients, with or without additional ST segment elevation, the ST segment declined significantly at 1 h (-1.0 +/- 1.7, P < 0.001, vs 0.1 +/- 1.5 mm, ns). CONCLUSIONS: Additional ST segment elevation is frequently observed during the first hour of intravenous thrombolysis with streptokinase. Its' association with a subsequent early decline of ST elevation, reduced mortality, a shorter time interval to peak creatine kinase, and a high rate of late recanalization, suggest that in some patients it is one of the earliest markers of reperfusion.

Adult↗
PubMed1988

Patterns of maximal spatial ST vector of S-T segment elevation in the right praecordial leads of the electrocardiogram in patients with acute inferior myocardial infarction.

Thirty patients with S-T segment elevation in the right praecordial leads during acute inferior myocardial infarction were studied by vectorcardiography. From the vectorcardiographic traces two types of maximal spatial ST vectors were seen. Their directions pointed either to: (1) the right-anterior-inferior, or (2) the right-posterior-inferior octant. This spatial ST vector could cause S-T segment elevation in the right praecordial leads in patients with acute inferior myocardial infarction in two ways. (1) The projection of the right-anterior-inferior maximal spatial ST vector on the horizontal plan pointing to right-anterior direction directly causes S-T segment elevation in the right praecordial leads--only a minority of patients (20%) show this. (2) The large magnitude of the right-posterior-inferior maximal spatial ST vector indirectly causes S-T segment elevation in the right praecordial leads adjacent to it. The majority of patients (80%) belong to this group. Therefore, the maximal S-T segment elevation in the electrocardiogram should be looked for in leads V5R to V8R. The direction of the vectors imply that in some patients there would be no S-T segment elevation in lead V4R. This study indicates that the use of S-T segment elevation in V4R, or several right praecordial leads, to claim that the maximal ST vector points to the right-anterior direction can be misleading. Without directional information, the use of single lead or several leads to detect the maximal spatial ST vector by a scalar electrocardiogram will give incomplete information.(ABSTRACT TRUNCATED AT 250 WORDS)

Bundle-Branch Block↗
PubMed1998

Prediction of membrane proteins based on classification of transmembrane segments.

The number of transmembrane segments often corresponds to a structural or functional class of membrane proteins such as to seven-transmembrane receptors and six-transmembrane ion channels. We have developed a new prediction method to detect the membrane protein class that is defined by the number of transmembrane segments, as well as to locate the transmembrane segments in the amino acid sequence. Each membrane protein class is represented by a model of ordering different types of transmembrane segments. Specifically, we have classified the transmembrane segments in known membrane proteins into five groups (types) using the Mahalanobis distance with the average hydrophobicity and the periodicity of hydrophobicity as a measure of similarity. The discriminant functions derived for these groups were then used to detect transmembrane segments and to match with the models for one- to fourteen-spanning membrane proteins and for globular proteins. Using the test data set of 89 membrane proteins whose transmembrane positions are known by experimental evidence, 61.8% of the proteins and 85.1% of the transmembrane segments were correctly predicted. Because of the new feature to predict membrane protein classes, the method should be useful in the functional assignment of genomic sequences.

Animals↗