MSACompro: protein multiple sequence alignment using predicted secondary structure, solvent accessibility, and residue-residue contacts

<p>Abstract</p> <p>Background</p> <p>Multiple Sequence Alignment (MSA) is a basic tool for bioinformatics research and analysis. It has been used essentially in almost all bioinformatics tasks such as protein structure modeling, gene and protein function prediction, DNA motif recognition, and phylogenetic analysis. Therefore, improving the accuracy of multiple sequence alignment is important for advancing many bioinformatics fields.</p> <p>Results</p> <p>We designed and developed a new method, MSACompro, to synergistically incorporate predicted secondary structure, relative solvent accessibility, and residue-residue contact information into the currently most accurate posterior probability-based MSA methods to improve the accuracy of multiple sequence alignments. The method is different from the multiple sequence alignment methods (e.g. 3D-Coffee) that use the tertiary structure information of some sequences since the structural information of our method is fully predicted from sequences. To the best of our knowledge, applying predicted relative solvent accessibility and contact map to multiple sequence alignment is novel. The rigorous benchmarking of our method to the standard benchmarks (i.e. BAliBASE, SABmark and OXBENCH) clearly demonstrated that incorporating predicted protein structural information improves the multiple sequence alignment accuracy over the leading multiple protein sequence alignment tools without using this information, such as MSAProbs, ProbCons, Probalign, T-coffee, MAFFT and MUSCLE. And the performance of the method is comparable to the state-of-the-art method PROMALS of using structural features and additional homologous sequences by slightly lower scores.</p> <p>Conclusion</p> <p>MSACompro is an efficient and reliable multiple protein sequence alignment tool that can effectively incorporate predicted protein structural information into multiple sequence alignment. The software is available at <url>http://sysbio.rnet.missouri.edu/multicom_toolbox/</url>.</p

Improving the Alignment Quality of Consistency Based Aligners with an Evaluation Function Using Synonymous Protein Words

Most sequence alignment tools can successfully align protein sequences with higher levels of sequence identity. The accuracy of corresponding structure alignment, however, decreases rapidly when considering distantly related sequences (<20% identity). In this range of identity, alignments optimized so as to maximize sequence similarity are often inaccurate from a structural point of view. Over the last two decades, most multiple protein aligners have been optimized for their capacity to reproduce structure-based alignments while using sequence information. Methods currently available differ essentially in the similarity measurement between aligned residues using substitution matrices, Fourier transform, sophisticated profile-profile functions, or consistency-based approaches, more recently

Views and experiences of people with intellectual disabilities regarding intimate relationships: a qualitative metasynthesis

The aims of this review were to systematically identify, critically appraise and synthesize the results of existing qualitative literature exploring the views and experiences of intimate relationships amongst people with intellectual disabilities. Fourteen peer-reviewed articles were identified through a systematic search of eight databases, reference lists, citations, and relevant journals. The identified articles were appraised for quality, then synthesized using a metaethnography approach. No study met all quality criteria and references to ethical approval were often lacking. Interpretation of the findings suggested three key themes: the meaning of intimate relationships, external constraints and facilitators, and managing external constraints. Though many people with intellectual disabilities desire and benefit from intimate relationships, they experience restrictions that others do not, which can lead to isolation and loneliness. Intimate relationships are not always necessarily linked with sexual behavior; therefore, intimate relationships warrant their own focus in future research, as well as in education and training for people with intellectual disabilities and their caregivers. Within this, a commitment to transparency over research processes is needed, in particular with reference to how ethical approval was obtained, since this has been a shortcoming of research with this focus to date

Mechanisms of blood homeostasis: lineage tracking and a neutral model of cell populations in rhesus macaques

BACKGROUND: How a potentially diverse population of hematopoietic stem cells (HSCs) differentiates and proliferates to supply more than 10(11) mature blood cells every day in humans remains a key biological question. We investigated this process by quantitatively analyzing the clonal structure of peripheral blood that is generated by a population of transplanted lentivirus-marked HSCs in myeloablated rhesus macaques. Each transplanted HSC generates a clonal lineage of cells in the peripheral blood that is then detected and quantified through deep sequencing of the viral vector integration sites (VIS) common within each lineage. This approach allowed us to observe, over a period of 4-12 years, hundreds of distinct clonal lineages. RESULTS: While the distinct clone sizes varied by three orders of magnitude, we found that collectively, they form a steady-state clone size-distribution with a distinctive shape. Steady-state solutions of our model show that the predicted clone size-distribution is sensitive to only two combinations of parameters. By fitting the measured clone size-distributions to our mechanistic model, we estimate both the effective HSC differentiation rate and the number of active HSCs. CONCLUSIONS: Our concise mathematical model shows how slow HSC differentiation followed by fast progenitor growth can be responsible for the observed broad clone size-distribution. Although all cells are assumed to be statistically identical, analogous to a neutral theory for the different clone lineages, our mathematical approach captures the intrinsic variability in the times to HSC differentiation after transplantation. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12915-015-0191-8) contains supplementary material, which is available to authorized users

Simulation of global warming effect on outdoor thermal comfort conditions

In the coming decades, global warming and increase in temperature, in different regions of the world, may change indoor and outdoor thermal comfort conditions and human health. The aim of this research was to study the effects of global warming on thermal comfort conditions in indoor ambiences in Iran. To study the increase in temperature, model for assessment of greenhouse-gas induced climate change scenario generator compound model has been used together with four scenarios and to estimate thermal comfort conditions, adaptive model of the American Society of Heating, Refrigerating and Air-conditioning Engineers has been used. In this study, Iran was divided into 30 zones, outdoor conditions were obtained using meteorological data of 80 climatological stations and changes in neutral comfort conditions in 2025, 2050, 2075 and 2100 were predicted. In accordance with each scenario, findings from this study showed that temperature in the 30 zones will increase by 2100 to between 3.4 °C and 5.6 °C. In the coming decades and in the 30 studied zones, neutral comfort temperature will increase and be higher and more intense in the central and desert zones of Iran. The low increase in this temperature will be connected to the coastal areas of the Caspian and Oman Sea in southeast Iran. This increase in temperature will be followed by a change in thermal comfort and indoor energy consumption from 8.6 % to 13.1 % in air conditioning systems. As a result, passive methods as thermal inertia are proposed as a possible solution

Simulation Of Temperature Changes In Iran Under The Atmosphere Carbon Dioxide Duplication Condition

The present research intends to show the effect of global warming on the trend and patterns of temperature in Iran. The study has been divided into two primary parts, the first of which is an analysis of the country&apos;s temperature trend using the following data measures: the minimum, maximum, and mean seasonal night temperature (the minimum temperature) components, the day temperature (the maximum temperature) component and the mean daily temperature component. This data is specific to the time frame 1951 to 2005 and it was obtained from 92 synoptic and climatology stations around the country. The second part of this research involved simulating and forecasting the effects of global warming on temperature values under conditions in which greenhouse gases have increased. For analyzing these simulations and forecasts the MAGICC SCENGEN model was used and different climate change scenarios were taken into consideration. The results are quite interesting. In the analysis of the country’s current temperature trend and in the forecasting’s, specifically related to time, a significant temperature increase was observed during the summer months. Also, with regard to altitudinal levels, it was evident that stations at higher altitudes show a more significant increase in daily and mean daily temperatures. Taking into account the output mean of the different climate change scenarios, the temperature simulations show a 4.41° C increase in Iran’s mean temperature by 2100. Most of these temperature increases would occur in the southern and eastern parts of Bushehr, certain coastal regions of the Persian Gulf, eastern and western parts of Fars, Kohgilooye, Boyerahmad, southern parts of Yazd, as well as southern and southeastern parts of Esfahan

Urban Sprawl And Climatic Changes In Tehran

Urban sprawl beginning in the developed countries around 1950 is currently experienced in almost all countries. Many studies on the effects of urban sprawl indicate the emergence of harmful effects of this phenomenon. One of the most important environmental effects is the changes in climate. The purpose of this research was to identify the relation between urban sprawl components of Tehran with changes in climate variables. To this end, two data sets have been used to study the relation between these elements and components. The first data set included climatic elements such as rainfall, temperature, the percent of relative humidity and the percent of calm wind, as well as its mean speed for a period of 54 years (1953-2006). The second set of data was formed by components relevant to urban sprawl such as city area, private cars per capita, population density and number of urban population. Pearson correlation and multiple regression methods have been applied to compare and identify the relation between climatic components with urban sprawl indices. Results of correlation indicate that among the 5 aforementioned climatic components, annual rainfall and the mean of wind speed do not appear to have significant relation with sprawl, but the oscillations in percent of relative humidity and percent of calm wind seem to have a significant relation with Tehran sprawl. Consequently and using multivariate regression, it was concluded that the most important factor in the increasing temperature of Tehran, is the number of cars; the most important factor in increasing the percent of relative humidity is the area of Tehran, whereas the increase of the percent of calm wind may be attributed to the increase of population

Effects Of Climate Change Process On Comfort Climate Of Shiraz Station

Dwelling in cities and city development together with quick increase of population and development of industrial activities with unplanned consumption of fossil fuel have intensively increased pollutions with consequences which will cause different diseases in short period, will lead to some climatic oscillations and its environmental effects such as the change of desirable periods in view of comfort climate in long period. The objective point of view of this research was to study the climate in Shiraz and its effect on comfort conditions for human physiology. In this research, using 55-year climatic data (1952-2006), the relative humidity and temperature through the application Guni comfort climatic model, the desirable months for the comfort of human physiology have been determined in the five 11-year periods and the linear process of these changes have been estimated for the next 11 years. The results of this research show that the temperature trend in Shiraz station is increasing and most months have heating process in a way that it is expected that in the coming future, the cold months will have more favoring conditions for physiological comfort of residents and correspondingly in the warm months, heating tension will have remarkable increase

Climate change and its role in forecasting energy demand in buildings: A case study of Douala City, Cameroon

The foremost role of a building is to assure the comfort of its occupants. The thermal comfort of a building depends on the outdoor climate and requires a demand in energy for heating and cooling. In this paper, demand of energy (heating/cooling) in the buildings is discussed in Douala, Cameroon. Daily data of the last 40 years coming from five weather stations of Cameroon have been studied. Some forecasts have been carried out with 14 GCM models, associated to three future climate scenarios B1, A2, and A1B. However, only INCM3 of General Circulation Model (GCM) and A2 scenario was used. Energy demand in buildings is valued by HDD (heating degree day) and CDD (cooling degree day) indices. Obtained results show that the temperature evolves more quickly in dry season than in rainy season in Douala. Climate rise indicates an increasing demand of energy in the buildings for cooling. Global Douala heating shows a definite effect on outdoor comfort. From 2045 to 2075, the demand of energy for cooling will be superior to 50%. The total demand in energy for heating in the buildings is estimated to be 67.882 kcal from 1970 to 2000 and will be around 67.774 kcal from 2013 to 2043