Dataset Information

Profile-profile comparisons by COMPASS predict intricate homologies between protein families.

ABSTRACT: Recently we proposed a novel method of alignment-alignment comparison, COMPASS (the tool for COmparison of Multiple Protein Alignments with Assessment of Statistical Significance). Here we present several examples of the relations between PFAM protein families that were detected by COMPASS and that lead to the predictions of presently unresolved protein structures. We discuss relatively straightforward COMPASS predictions that are new and interesting to us, and that would require a substantial time and effort to justify even for a skilled PSI-BLAST user. All of the presented COMPASS hits are independently confirmed by other methods, including the ab initio structure-prediction method ROSETTA. The tertiary structure predictions made by ROSETTA proved to be useful for improving sequence-derived alignments, because they are based on a reasonable folding of the polypeptide chain rather than on the information from sequence databases. The ability of COMPASS to predict new relations within the PFAM database indicates the high sensitivity of COMPASS searches and substantiates its potential value for the discovery of previously unknown similarities between protein families.

SUBMITTER: Sadreyev RI

PROVIDER: S-EPMC2366929 | biostudies-literature | 2003 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Profile-profile comparisons by COMPASS predict intricate homologies between protein families.

Sadreyev Ruslan I RI Baker David D Grishin Nick V NV

Protein science : a publication of the Protein Society 20031001 10

Recently we proposed a novel method of alignment-alignment comparison, COMPASS (the tool for COmparison of Multiple Protein Alignments with Assessment of Statistical Significance). Here we present several examples of the relations between PFAM protein families that were detected by COMPASS and that lead to the predictions of presently unresolved protein structures. We discuss relatively straightforward COMPASS predictions that are new and interesting to us, and that would require a substantial t ...[more]

PMID: 14500884

Similar Datasets

Project description:BACKGROUND:Obesity is a risk factor for colorectal cancer, yet metabolic distinctions between healthy right and left colon tissue, before cancer is diagnosed, remains largely unknown. This study compared right-ascending and left-descending colon tissue metabolomes to identify differences from the stool metabolome in normal weight, overweight, and obese adults. AIM:To examine right and left colon tissue metabolites according to body mass index that may serve as mechanistic targets for interventions and biomarkers for colon cancer risk. METHODS:Global, non-targeted metabolomics was applied to assess right-ascending and left-descending colon tissue collected from healthy adults undergoing screening colonoscopies to test the hypothesis that BMI differentially impacts colon tissue metabolite profiles. The colon tissue and stool metabolome of healthy adults (n = 24) was analyzed for metabolite signatures and metabolic pathway networks implicated in progression of colorectal cancer. RESULTS:Ascending and descending colon contained 504 host, food, and microbiota-derived metabolites from normal weight, overweight and obese adults grouped according to body mass index. Amino acids, lipids, and nucleotides were among the chemical types that further differentiated from the stool metabolite profiles. Normal weight adults had 46 significantly different metabolites between ascending and descending colon tissue locations, whereas there were 37 metabolite differences in overweight and 28 metabolite differences for obese adults (P < 0.05). Obese adults had trimethylamine N-oxide, endocannabinoids and monoacylglycerols with different relative abundances identified between ascending and descending colon. Primary and secondary bile acids, vitamins, and fatty acids also showed marked relative abundance differences in colon tissue from overweight/obese adults. CONCLUSION:There were metabolite profile differences between right-ascending and left-descending colon tissue in healthy adults. Colon lipids and other metabolites in obese and overweight adults were distinguished from normal weight participants and associated with gut inflammation, nutrient absorption, and products of microbiota metabolism.

Project description:BackgroundMothers and children in families with one immigrant parent have been reported to be healthier than those in native families; however, the health of the fathers in these families has rarely been discussed in literature.ObjectiveWe aimed to comprehensively compare the health of all the family members between families with one immigrant parent (native fathers, immigrant mothers, and their children) and native families (native fathers, native mothers, and their children).MethodsWe conducted a cohort study by using the Taiwan Maternal and Child Health Database to recruit live-born children and their parents from 2004 to 2016. Overall, we identified 90,670 fathers, 91,270 mothers, and 132,457 children in families with one immigrant parent and 1,666,775 fathers, 1,734,104 mothers, and 2,637,191 children in native families and followed up with them from 2004 to 2017. The outcomes comprised common physical and mental disorders, catastrophic illnesses, mortality, and child adversities and accidents. The covariates comprised the child's year of birth, parental age, low-income status, and physical or mental disorder status. Logistic regression was performed to compare the risks of the outcomes between families with one immigrant parent and native families.ResultsThe parents in families with one immigrant parent were more likely to be of low-income status and were older than the parents in native families. After adjusting for the covariates, fathers in families with one immigrant parent were found to have higher risks of physical and mental disorders, catastrophic illness, and mortality than fathers in native families. Conversely, mothers in families with one immigrant parent had lower risks of physical and mental disorders, catastrophic illness, and mortality than mothers in native families. Finally, the children in families with one immigrant parent generally had better physical and mental health but higher risks for leukemia, liver diseases, autism spectrum disorder, and road traffic accidents than children in native families.ConclusionsThe health status of the members of families with one immigrant parent was nonhomogeneous, and the poorer general health of fathers in such families suggests health inequalities in families with one immigrant parent.

Project description:PurposeThe ChicagO Multiethnic Prevention and Surveillance Study or 'COMPASS' is a population-based cohort study with a goal to examine the risk and determinants of cancer and chronic disease. COMPASS aims to address factors causing and/or exacerbating health disparities using a precision health approach by recruiting diverse participants in Chicago, with an emphasis on those historically underrepresented in biomedical research.ParticipantsNearly 8000 participants have been recruited from 72 of the 77 Chicago community areas. Enrolment entails the completion of a 1-hour long survey, consenting for past and future medical records from all sources, the collection of clinical and physical measurement data and the on-site collection of biological samples including blood, urine and saliva. Indoor air monitoring data and stool samples are being collected from a subset of participants. On collection, all biological samples are processed and aliquoted within 24 hours before long-term storage and subsequent analysis.Findings to dateThe cohort reported an average age of 53.7 years, while 80.5% identified as African-American, 5.7% as Hispanic and 47.8% as men. Over 50% reported earning less than US$15 000 yearly, 35% were obese and 47.8% were current smokers. Moreover, 38% self-reported having had a diagnosis of hypertension, while 66.4% were measured as hypertensive at enrolment.Future plansWe plan to expand recruitment up to 100 000 participants from the Chicago metropolitan area in the next decade using a hybrid community and clinic-based recruitment framework that incorporates data collection through mobile medical units. Follow-up data collection from current cohort members will include serial samples, as well as longitudinal health, lifestyle and behavioural assessment. We will supplement self-reported data with electronic medical records, expand the collection of biometrics and biosamples to facilitate increasing digital epidemiological study designs and link to state and/or national level databases to ascertain outcomes. The results and findings will inform potential opportunities for precision disease prevention and mitigation in Chicago and other urban areas with a diverse population.RegistrationNA.

Project description:MotivationViruses infect, reprogram, and kill microbes, leading to profound ecosystem consequences, from elemental cycling in oceans and soils to microbiome-modulated diseases in plants and animals. Although metagenomic datasets are increasingly available, identifying viruses in them is challenging due to poor representation and annotation of viral sequences in databases.ResultsHere we establish efam, an expanded collection of Hidden Markov Model (HMM) profiles that represent viral protein families conservatively identified from the Global Ocean Virome 2.0 dataset. This resulted in 240,311 HMM profiles, each with at least 2 protein sequences, making efam >7-fold larger than the next largest, pan-ecosystem viral HMM profile database. Adjusting the criteria for viral contig confidence from "conservative" to "eXtremely Conservative" resulted in 37,841 HMM profiles in our efam-XC database. To assess the value of this resource, we integrated efam-XC into VirSorter viral discovery software to discover viruses from less-studied, ecologically distinct oxygen minimum zone (OMZ) marine habitats. This expanded database led to an increase in viruses recovered from every tested OMZ virome by ∼24% on average (up to ∼42%) and especially improved the recovery of often-missed shorter contigs (<5 kb). Additionally, to help elucidate lesser-known viral protein functions, we annotated the profiles using multiple databases from the DRAM pipeline and virion-associated metaproteomic data, which doubled the number of annotations obtainable by standard, single-database annotation approaches. Together, these marine resources (efam and efam-XC) are provided as searchable, compressed HMM databases that will be updated bi-annually to help maximize viral sequence discovery and study from any ecosystem.AvailabilityThe resources are available on the iVirus platform at (doi.org/10.25739/9vze-4143).Supplementary informationSupplementary data are available at Bioinformatics online.

Project description:BackgroundIn many countries smoking rates have declined and obesity rates have increased, and social inequalities in each have varied over time. At the same time, mortality has declined in most high-income countries, but gaps by educational qualification persist-at least partially due to differential smoking and obesity distributions. This study uses a compass typology to simultaneously examine the magnitude and trends in educational inequalities across multiple countries in: a) smoking and obesity; b) smoking-related mortality and c) cause-specific mortality.MethodsSmoking prevalence, obesity prevalence and cause-specific mortality rates (35-79 year olds by sex) in nine European countries and New Zealand were sourced from between 1980 and 2010. We calculated relative and absolute inequalities in prevalence and mortality (relative and slope indices of inequality, respectively RII, SII) by highest educational qualification. Countries were then plotted on a compass typology which simultaneously examines trends in the population average rates or odds on the x-axis, RII on the Y-axis, and contour lines depicting SII.FindingsSmoking and obesity. Smoking prevalence in men decreased over time but relative inequalities increased. For women there were fewer declines in smoking prevalence and relative inequalities tended to increase. Obesity prevalence in men and women increased over time with a mixed picture of increasing absolute and sometimes relative inequalities. Absolute inequalities in obesity increased for men and women in Czech Republic, France, New Zealand, Norway, for women in Austria and Lithuania, and for men in Finland. Cause-specific mortality. Average rates of smoking-related mortality were generally stable or increasing for women, accompanied by increasing relative inequalities. For men, average rates were stable or decreasing, but relative inequalities increased over time. Cardiovascular disease, cancer, and external injury rates generally decreased over time, and relative inequalities increased. In Eastern European countries mortality started declining later compared to other countries, however it remained at higher levels; and absolute inequalities in mortality increased whereas they were more stable elsewhere.ConclusionsTobacco control remains vital for addressing social inequalities in health by education, and focus on the least educated is required to address increasing relative inequalities. Increasing obesity in all countries and increasing absolute obesity inequalities in several countries is concerning for future potential health impacts. Obesity prevention may be increasingly important for addressing health inequalities in some settings. The compass typology was useful to compare trends in inequalities because it simultaneously tracks changes in rates/odds, and absolute and relative inequality measures.

Dataset Information

Profile-profile comparisons by COMPASS predict intricate homologies between protein families.

Publications

Profile-profile comparisons by COMPASS predict intricate homologies between protein families.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets