Pub Date : 2021-01-01Epub Date: 2021-08-23DOI: 10.14806/ej.26.1.974
Marilena Panagiotou, Maria Charalampopoulou, Flora Bacopoulou, Ioanna Maria Velegraki, Ioulia Kokka, Dimitrios Vlachakis, George P Chrousos, Christina Darviri
Bullying among children and adolescents can have detrimental effects on their physical and mental health. The first step in the identification of bullying is the detection of relevant signs and behaviours, with the use of appropriate instruments. The widely used Peer Relation Questionnaire (PRQ)has been developed to measure bullying behaviour in children and adolescents. The aim of this study was to translate and validate this instrument in the Greek language in a school sample of children and adolescents. A sample of 193 students (mean age ± SD 11.44 ± 1.26 years, girls 49.7%), was recruited from elementary and junior high schools of the public and private sector, in the capital of Athens, Greece. Along with the Peer Relation Questionnaire, the Stress in Children questionnaire and a structured inquiry regarding satisfaction from various aspects of life were used to assess the criterion validity of the Peer Relation Questionnaire. Results revealed good psychometric properties of the questionnaire in the Greek language. The principal component analysis resulted in two subscales that demonstrated an adequate internal consistency and a significant correlation with stress and satisfaction parameters, suggesting satisfying criterion validity. Meaningful associations between demographic characteristics and the subscales were also found. The Greek version of the Peer Relation Questionnaire-short form can be used as a valid tool to measure bullying behaviour in children and adolescents.
{"title":"Reliability and validity of the Peer Relation Questionnaire in a sample of Greek school children and adolescents.","authors":"Marilena Panagiotou, Maria Charalampopoulou, Flora Bacopoulou, Ioanna Maria Velegraki, Ioulia Kokka, Dimitrios Vlachakis, George P Chrousos, Christina Darviri","doi":"10.14806/ej.26.1.974","DOIUrl":"10.14806/ej.26.1.974","url":null,"abstract":"<p><p>Bullying among children and adolescents can have detrimental effects on their physical and mental health. The first step in the identification of bullying is the detection of relevant signs and behaviours, with the use of appropriate instruments. The widely used Peer Relation Questionnaire (PRQ)has been developed to measure bullying behaviour in children and adolescents. The aim of this study was to translate and validate this instrument in the Greek language in a school sample of children and adolescents. A sample of 193 students (mean age ± SD 11.44 ± 1.26 years, girls 49.7%), was recruited from elementary and junior high schools of the public and private sector, in the capital of Athens, Greece. Along with the Peer Relation Questionnaire, the Stress in Children questionnaire and a structured inquiry regarding satisfaction from various aspects of life were used to assess the criterion validity of the Peer Relation Questionnaire. Results revealed good psychometric properties of the questionnaire in the Greek language. The principal component analysis resulted in two subscales that demonstrated an adequate internal consistency and a significant correlation with stress and satisfaction parameters, suggesting satisfying criterion validity. Meaningful associations between demographic characteristics and the subscales were also found. The Greek version of the Peer Relation Questionnaire-short form can be used as a valid tool to measure bullying behaviour in children and adolescents.</p>","PeriodicalId":72893,"journal":{"name":"EMBnet.journal","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8494435/pdf/nihms-1742270.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39498242","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-01-01Epub Date: 2021-10-22DOI: 10.14806/ej.26.1.981
Maria Zarenti, Evangelia Kressou, Zacharo Panagopoulou, Flora Bacopoulou, Ioulia Kokka, Dimitrios Vlachakis, George P Chrousos, Christina Darviri
Cancer is considered one of the dominant life-threatening diseases in children. Working in the field of pediatric oncology, although rewarding, can be a source of stress and emotional burden for health care providers. The aim of this systematic review was to summarise the evidence regarding the occupational stress of health care providers working with pediatric cancer patients. Extensive search of the Pubmed and Scopus databases was performed to identify studies relevant to the topic. Initial search retrieved 657 studies. The reviewing investigators, after applying the inclusion/exclusion criteria, extracted data to critically appraise the quality of evidence. The final step of search concluded in 23 studies of heterogeneous design. Results revealed two main domains of which occupational stress derived from i) the interaction of the health care provider with the patient and the family, and ii) several organisational factors, such as hierarchical structures, experience, workload, and low organisational support. Literature on the stress of pediatric oncology staff is limited. The rather small sample sizes of the studies, the heterogeneity of methodological design, the lack of assessment from a sociological point of view, as well as the limited psychometric instruments adapted to pediatric oncology staff, make the validity of the results questionable. Further research is warranted to obtain a more accurate view of the field, to identify a cause-effect relation between work-related stress and pediatric oncology staff, and, more importantly, to guide future recommendations on support systems and stress management training within pediatric oncology settings.
{"title":"Stress among pediatric oncology staff. A systematic review.","authors":"Maria Zarenti, Evangelia Kressou, Zacharo Panagopoulou, Flora Bacopoulou, Ioulia Kokka, Dimitrios Vlachakis, George P Chrousos, Christina Darviri","doi":"10.14806/ej.26.1.981","DOIUrl":"10.14806/ej.26.1.981","url":null,"abstract":"<p><p>Cancer is considered one of the dominant life-threatening diseases in children. Working in the field of pediatric oncology, although rewarding, can be a source of stress and emotional burden for health care providers. The aim of this systematic review was to summarise the evidence regarding the occupational stress of health care providers working with pediatric cancer patients. Extensive search of the Pubmed and Scopus databases was performed to identify studies relevant to the topic. Initial search retrieved 657 studies. The reviewing investigators, after applying the inclusion/exclusion criteria, extracted data to critically appraise the quality of evidence. The final step of search concluded in 23 studies of heterogeneous design. Results revealed two main domains of which occupational stress derived from i) the interaction of the health care provider with the patient and the family, and ii) several organisational factors, such as hierarchical structures, experience, workload, and low organisational support. Literature on the stress of pediatric oncology staff is limited. The rather small sample sizes of the studies, the heterogeneity of methodological design, the lack of assessment from a sociological point of view, as well as the limited psychometric instruments adapted to pediatric oncology staff, make the validity of the results questionable. Further research is warranted to obtain a more accurate view of the field, to identify a cause-effect relation between work-related stress and pediatric oncology staff, and, more importantly, to guide future recommendations on support systems and stress management training within pediatric oncology settings.</p>","PeriodicalId":72893,"journal":{"name":"EMBnet.journal","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8623911/pdf/nihms-1754040.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39941543","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
D. D’Elia, C. Evelo, B. Regierer, Susanne Hollmann
On the 2 March 2020, the COST Action - Harmonising standardisation strategies to increase efficiency and competitiveness of European life-science research (CHARME) - held its final conference in Brussels After four years of successful work, the members of the COST Action CHARME met in Brussels to summarise the achievements and to discuss future perspectives and challenges for standardisation in the life sciences. Following the motto "Standards make the world go round", the outcomes of the COST Action are manifold and introduced some basic concepts and definitions that support a better understanding of the challenges and requirements. The results of this COST Action's network will be subject of a White Paper addressing the needs of standardisation, including a catalogue of requirements and recommendations to be disseminated to decision-makers at all levels to enable the implementation of standards in the daily workflow of research in academia and industry. The Action, ending this month, has given the opportunity to its members to tentatively presenting a set of preliminary requirements to develop further the harmonisation of standards. We hope this will inspire other Actions for the future.
{"title":"Standards make the world go round","authors":"D. D’Elia, C. Evelo, B. Regierer, Susanne Hollmann","doi":"10.14806/ej.25.0.931","DOIUrl":"https://doi.org/10.14806/ej.25.0.931","url":null,"abstract":"On the 2 March 2020, the COST Action - Harmonising standardisation strategies to increase efficiency and competitiveness of European life-science research (CHARME) - held its final conference in Brussels After four years of successful work, the members of the COST Action CHARME met in Brussels to summarise the achievements and to discuss future perspectives and challenges for standardisation in the life sciences. Following the motto \"Standards make the world go round\", the outcomes of the COST Action are manifold and introduced some basic concepts and definitions that support a better understanding of the challenges and requirements. The results of this COST Action's network will be subject of a White Paper addressing the needs of standardisation, including a catalogue of requirements and recommendations to be disseminated to decision-makers at all levels to enable the implementation of standards in the daily workflow of research in academia and industry. The Action, ending this month, has given the opportunity to its members to tentatively presenting a set of preliminary requirements to develop further the harmonisation of standards. We hope this will inspire other Actions for the future.","PeriodicalId":72893,"journal":{"name":"EMBnet.journal","volume":"22 3 1","pages":"931"},"PeriodicalIF":0.0,"publicationDate":"2020-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83932453","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Viviane Nguefack Ngoune, Perrine Pégorier, M. Bertignac, Imène Chentli, V. Giudicelli, Saida Hadi-Saljoqi, J. Jabado-Michaloud, G. Folch
IMGT®, the international ImMunoGeneTics information system® (http://www.imgt.org), is the global reference in immunogenetics and immunoinformatics. In 2019, for the first time, two pupils were welcomed within the team and introduced to immunoinformatics thank to the «Apprentis Chercheurs » programme founded by the association «l’Arbre des Connaissances ». This article describes the method and pedagogical approaches used, and demonstrates that immunoinformatics can be successfully taught to pupils of middle and high school.
IMGT®,国际免疫遗传学信息系统®(http://www.imgt.org),是免疫遗传学和免疫信息学的全球参考。2019年,团队首次欢迎两名学生加入,并感谢“arbre des Connaissances”协会创立的“学徒Chercheurs”计划,向他们介绍了免疫信息学。本文描述了免疫信息学的方法和教学方法,并证明免疫信息学可以成功地教授给初高中学生。
{"title":"Immunoinformatics taught to middle and high school pupils in IMGT®","authors":"Viviane Nguefack Ngoune, Perrine Pégorier, M. Bertignac, Imène Chentli, V. Giudicelli, Saida Hadi-Saljoqi, J. Jabado-Michaloud, G. Folch","doi":"10.14806/ej.25.1.926","DOIUrl":"https://doi.org/10.14806/ej.25.1.926","url":null,"abstract":"IMGT®, the international ImMunoGeneTics information system® (http://www.imgt.org), is the global reference in immunogenetics and immunoinformatics. In 2019, for the first time, two pupils were welcomed within the team and introduced to immunoinformatics thank to the «Apprentis Chercheurs » programme founded by the association «l’Arbre des Connaissances ». This article describes the method and pedagogical approaches used, and demonstrates that immunoinformatics can be successfully taught to pupils of middle and high school. ","PeriodicalId":72893,"journal":{"name":"EMBnet.journal","volume":"48 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86738678","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-01-01Epub Date: 2020-08-04DOI: 10.14806/ej.26.0.934
Thanasis Mitsis, Katerina Pierouli, Kalliopi Lo Diakou, Eleni Papakonstantinou, Flora Bacopoulou, George P Chrousos, Dimitrios Vlachakis
Extracellular vesicles have been the focus of a large number of studies in the past five years. Exosomes, a subgroup of extracellular vesicles, are of particularly high interest because they partake in a wide number of biological pathways. Produced by a variety of cells, exosomes have an important role in both physiological and pathological conditions. Exosome cargo heavily defines the vesicles' unique characteristics, and the cargo with the most intriguing prospects in its' biomedical applications is the non-coding RNAs. Non-coding RNAs, and specifically microRNAs are implicated in the regulation of many biological processes and have been associated with numerous diseases. Exosomes containing such important cargo can be used as biomarkers, therapeutic biomaterials, or even drug carriers. The potential media use of exosomes seems promising. However, some obstacles should be overcome before their clinical application. Synthetic exosome-like biomolecules may be a solution, but their production is still in their beginning stages. This review provides concise information regarding the current trends in exosome studies.
{"title":"Exosomics.","authors":"Thanasis Mitsis, Katerina Pierouli, Kalliopi Lo Diakou, Eleni Papakonstantinou, Flora Bacopoulou, George P Chrousos, Dimitrios Vlachakis","doi":"10.14806/ej.26.0.934","DOIUrl":"10.14806/ej.26.0.934","url":null,"abstract":"<p><p>Extracellular vesicles have been the focus of a large number of studies in the past five years. Exosomes, a subgroup of extracellular vesicles, are of particularly high interest because they partake in a wide number of biological pathways. Produced by a variety of cells, exosomes have an important role in both physiological and pathological conditions. Exosome cargo heavily defines the vesicles' unique characteristics, and the cargo with the most intriguing prospects in its' biomedical applications is the non-coding RNAs. Non-coding RNAs, and specifically microRNAs are implicated in the regulation of many biological processes and have been associated with numerous diseases. Exosomes containing such important cargo can be used as biomarkers, therapeutic biomaterials, or even drug carriers. The potential media use of exosomes seems promising. However, some obstacles should be overcome before their clinical application. Synthetic exosome-like biomolecules may be a solution, but their production is still in their beginning stages. This review provides concise information regarding the current trends in exosome studies.</p>","PeriodicalId":72893,"journal":{"name":"EMBnet.journal","volume":"26 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7440046/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38294085","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Dark Suite is a complete interactive software pipeline aiming to exploit the advantages of free software and modern programming. Besides two commands (installation and opening) on the command line, the handling and the program operation is done through a user's friendly interface. This platform has a central graphical interface which allows the user to choose in what computational tool to work. Each computational tool has an interface. Dark Suite combines the functions of other programmes to create a pipeline for high-quality secondary effects through a friendly user interface. It is made to run on GNU / Linux distributions and its interface was built using JAVA to seamlessly integrate scientific tools written in Perl, Java, R and Python.
Dark Suite是一个完整的交互式软件管道,旨在利用自由软件和现代编程的优势。除了命令行上的两个命令(安装和打开),处理和程序操作都是通过用户友好的界面完成的。该平台有一个中央图形界面,允许用户选择使用哪种计算工具。每个计算工具都有一个接口。Dark Suite结合了其他程序的功能,通过友好的用户界面创建了高质量的二次效果管道。它是在GNU / Linux发行版上运行的,它的界面是用JAVA构建的,可以无缝地集成用Perl、JAVA、R和Python编写的科学工具。
{"title":"Dark Suite: a comprehensive toolbox for computer-aided drug design.","authors":"Eleni Papakonstantinou, Vasileios Megalooikonomou, Dimitrios Vlachakis","doi":"10.14806/ej.25.0.928","DOIUrl":"https://doi.org/10.14806/ej.25.0.928","url":null,"abstract":"<p><p>Dark Suite is a complete interactive software pipeline aiming to exploit the advantages of free software and modern programming. Besides two commands (installation and opening) on the command line, the handling and the program operation is done through a user's friendly interface. This platform has a central graphical interface which allows the user to choose in what computational tool to work. Each computational tool has an interface. Dark Suite combines the functions of other programmes to create a pipeline for high-quality secondary effects through a friendly user interface. It is made to run on GNU / Linux distributions and its interface was built using JAVA to seamlessly integrate scientific tools written in Perl, Java, R and Python.</p>","PeriodicalId":72893,"journal":{"name":"EMBnet.journal","volume":"25 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7164806/pdf/nihms-1576509.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37849979","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
To evaluate the potency of potential helicase modulators, we developed an assay of helicase enzyme activity. Using a DNA or RNA biotin labelled oligonucleotide and after the addition of a recombinant helicase, the nucleic acid unwinds, causing the emission of luminescence, which is quantified with a particular antibody. In our assay, one of the DNA oligos was biotinylated, while the other was labelled with digoxygenin (DIG), both in their 5' termini. The biotin molecule immobilises the DNA duplex on a neutravidin-coated plate and the helicase activity is measured through the unwinding of DNA, due to ATP activation. The subsequent release of DIG-labelled oligos results in a luminescence signal measured with a chemiluminescence antibody. Our goal was to provide a high throughput screening method for potential helicase inhibitors. The method described in this paper has been demonstrated to be fast, easy and reproducible and doesn't use radiochemicals.
{"title":"An in silico and in vitro pipeline for the rapid screening of helicase modulators.","authors":"Eleni Papakonstantinou, Flora Bacopoulou, Vasileios Megalooikonomou, Aspasia Efthimiadou, Dimitrios Vlachakis","doi":"10.14806/ej.25.0.927","DOIUrl":"https://doi.org/10.14806/ej.25.0.927","url":null,"abstract":"<p><p>To evaluate the potency of potential helicase modulators, we developed an assay of helicase enzyme activity. Using a DNA or RNA biotin labelled oligonucleotide and after the addition of a recombinant helicase, the nucleic acid unwinds, causing the emission of luminescence, which is quantified with a particular antibody. In our assay, one of the DNA oligos was biotinylated, while the other was labelled with digoxygenin (DIG), both in their 5' termini. The biotin molecule immobilises the DNA duplex on a neutravidin-coated plate and the helicase activity is measured through the unwinding of DNA, due to ATP activation. The subsequent release of DIG-labelled oligos results in a luminescence signal measured with a chemiluminescence antibody. Our goal was to provide a high throughput screening method for potential helicase inhibitors. The method described in this paper has been demonstrated to be fast, easy and reproducible and doesn't use radiochemicals.</p>","PeriodicalId":72893,"journal":{"name":"EMBnet.journal","volume":"25 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7079759/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37753483","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yonas Kassahun Hirutu, Mesert D Bayeleygne, A. Desta, Tewodros Tariku, M. Abebe
Basic bioinformatics training workshop conducted at Armauer Hansen Research Institute (AHRI), Addis Ababa, Ethiopia. This report describes a bioinformatics training initiative started at AHRI aiming to support life science researchers and postgraduates in handling next-generation sequencing data.
{"title":"Training workshop on Mycobacterium whole genome sequence data analysis","authors":"Yonas Kassahun Hirutu, Mesert D Bayeleygne, A. Desta, Tewodros Tariku, M. Abebe","doi":"10.14806/ej.24.0.920","DOIUrl":"https://doi.org/10.14806/ej.24.0.920","url":null,"abstract":"Basic bioinformatics training workshop conducted at Armauer Hansen Research Institute (AHRI), Addis Ababa, Ethiopia. This report describes a bioinformatics training initiative started at AHRI aiming to support life science researchers and postgraduates in handling next-generation sequencing data.","PeriodicalId":72893,"journal":{"name":"EMBnet.journal","volume":"57 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85962518","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yoan Bouzin, B. Viart, M. Moriel-Carretero, S. Kossida
Python Function uncover (PyFuncover) is a new bioinformatic tool able to search proteins with a specific function in a full proteome. The pipeline coded in python uses BLAST alignment and the sequences from a PFAM family as the search seed. We tested PyFuncover using the fatty acid-binding family (FABP) Lipocalin_7 from PFAM (version 32, 2019) against the Homo sapiens NCBI proteome. After applying the scoring function in all the BLAST results, the data were classified and submitted to a GO-TERM analysis using bioDBnet. Analyses showed that all families of FABPs were ranked within the top scores. Included within this category were also families able to bind to hydrophobic molecules similar to fatty acids such as the retinol acid transporter and the cellular retinoic acid-binding protein.
Python Function discover (PyFuncover)是一种新的生物信息学工具,能够在完整的蛋白质组中搜索具有特定功能的蛋白质。用python编码的管道使用BLAST对齐和来自PFAM族的序列作为搜索种子。我们使用PFAM(版本32,2019)中的脂肪酸结合家族(FABP) Lipocalin_7对智人NCBI蛋白质组进行了PyFuncover测试。在对所有BLAST结果应用评分函数后,对数据进行分类并使用bioDBnet提交GO-TERM分析。分析显示,所有fabp家庭的得分都在前列。这一类中还包括能够与类似脂肪酸的疏水分子结合的家族,如视黄醇酸转运体和细胞视黄酸结合蛋白。
{"title":"PyFuncover: full proteome search for a specific function using BLAST and PFAM","authors":"Yoan Bouzin, B. Viart, M. Moriel-Carretero, S. Kossida","doi":"10.14806/EJ.24.0.925","DOIUrl":"https://doi.org/10.14806/EJ.24.0.925","url":null,"abstract":"Python Function uncover (PyFuncover) is a new bioinformatic tool able to search proteins with a specific function in a full proteome. The pipeline coded in python uses BLAST alignment and the sequences from a PFAM family as the search seed. We tested PyFuncover using the fatty acid-binding family (FABP) Lipocalin_7 from PFAM (version 32, 2019) against the Homo sapiens NCBI proteome. After applying the scoring function in all the BLAST results, the data were classified and submitted to a GO-TERM analysis using bioDBnet. Analyses showed that all families of FABPs were ranked within the top scores. Included within this category were also families able to bind to hydrophobic molecules similar to fatty acids such as the retinol acid transporter and the cellular retinoic acid-binding protein.","PeriodicalId":72893,"journal":{"name":"EMBnet.journal","volume":"29 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72409624","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}