Background: The right sampling of homologous sequences for phylogenetic or molecular evolution analyses is a crucial step, the quality of which can have a significant impact on the final interpretation of the study. T...
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Background: The right sampling of homologous sequences for phylogenetic or molecular evolution analyses is a crucial step, the quality of which can have a significant impact on the final interpretation of the study. There is no single way for constructing datasets suitable for phylogenetic analysis, because this task intimately depends on the scientific question we want to address, Moreover, database mining softwares such as BLAST which are routinely used for searching homologous sequences are not specifically optimized for this task. Results: To fill this gap, we designed BLAST-Explorer, an original and friendly web-based application that combines a BLAST search with a suite of tools that allows interactive, phylogenetic-oriented exploration of the BLAST results and flexible selection of homologous sequences among the BLAST hits. Once the selection of the BLAST hits is done using BLAST-Explorer, the corresponding sequence can be imported locally for external analysis or passed to the phylogenetic tree reconstruction pipelines available on the *** platform. Conclusions: BLAST-Explorer provides a simple, intuitive and interactive graphical representation of the BLAST results and allows selection and retrieving of the BLAST hit sequences based a wide range of criterions. Although BLAST-Explorer primarily aims at helping the construction of sequence datasets for further phylogenetic study, it can also be used as a standard BLAST server with enriched output. BLAST-Explorer is available at http://***
Background: The genus Pseudomonas comprises more than 100 species of environmental, clinical, agricultural, and biotechnological interest. Although, the recommended method for discriminating bacterial species is DNA-D...
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Background: The genus Pseudomonas comprises more than 100 species of environmental, clinical, agricultural, and biotechnological interest. Although, the recommended method for discriminating bacterial species is DNA-DNA hybridisation, alternative techniques based on multigenic sequence analysis are becoming a common practice in bacterial species discrimination studies. Since there is not a general criterion for determining which genes are more useful for species resolution;the number of strains and genes analysed is increasing continuously. As a result, sequences of different genes are dispersed throughout several databases. This sequence information needs to be collected in a common database, in order to be useful for future identification-based projects. Description: The PseudoMLSA Database is a comprehensive database of multiple gene sequences from strains of Pseudomonas species. The core of the database is composed of selected gene sequences from all Pseudomonas type strains validly assigned to the genus through 2008. The database is aimed to be useful for MultiLocus Sequence Analysis (MLSA) procedures, for the identification and characterisation of any Pseudomonas bacterial isolate. The sequences are available for download via a direct connection to the National Center for Biotechnology Information (NCBI). Additionally, the database includes an online BLAST interface for flexible nucleotide queries and similarity searches with the user's datasets, and provides a user-friendly output for easily parsing, navigating, and analysing BLAST results. Conclusions: The PseudoMLSA database amasses strains and sequence information of validly described Pseudomonas species, and allows free querying of the database via a user-friendly, web-based interface available at http://***/microbiologiaBD/***. The web-based platform enables easy retrieval at strain or gene sequence information level;including references to published peer-reviewed articles, and direct ext
The fundamental unit of protein structure is the domain, defined as a region or regions of a polypeptide that folds independently and possesses a hydrophobic core with a hydrophilic exterior (seeNote 1). Domains, part...
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The fundamental unit of protein structure is the domain, defined as a region or regions of a polypeptide that folds independently and possesses a hydrophobic core with a hydrophilic exterior (seeNote 1). Domains, particularly those with enzymatic activities, may possess functions independently of whether they are present in isolation or are part of a larger multidomain protein. Other domains confer regulatory and specificity properties to multidomain proteins, usually via the provision of binding sites. Because the majority of eukaryotic proteins, and a large number of eubacterial and archaeal proteins, are multidomain in character, the determination of the structures and functions of these proteins requires detailed consideration of their domain architectures. less
The purpose of this chapter is to illustrate how to obtain information on DNA and protein sequences from databases. This is most conveniently achieved using a Web browser (Netscape or Internet Explorer). This chapter ...
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The purpose of this chapter is to illustrate how to obtain information on DNA and protein sequences from databases. This is most conveniently achieved using a Web browser (Netscape or Internet Explorer). This chapter is loosely based on a course given by the author at the University of Hertfordshire from a set of Web pages that facilitate Internet navigation by using hyperlinks and allow sequences to be copied from the Web page and pasted into the relevant search engine. (The online version of this information can be found at http://***/natsci/Bio/*** .)The purpose of this chapter is to illustrate how to obtain information on DNA and protein sequences from databases. This is most conveniently achieved using a Web browser (Netscape or Internet Explorer). This chapter is loosely based on a course given by the author at the University of Hertfordshire from a set of Web pages that facilitate Internet navigation by using hyperlinks and allow sequences to be copied from the Web page and pasted into the relevant search engine. (The online version of this information can be found at http://***/natsci/Bio/*** .)
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