Multiple sequence alignments are successfully applied in many studies for understanding the structural and functional relations among single nucleic acids and protein sequences as well as whole families. Because of th...Multiple sequence alignments are successfully applied in many studies for understanding the structural and functional relations among single nucleic acids and protein sequences as well as whole families. Because of the rapid growth of sequence databases, multiple sequence alignments can often be very large and difficult to visualize and analyze. We offer a new service aimed to visualize and analyze the multiple alignments obtained with different external algorithms, with new features useful for the comparison of the aligned sequences as well as for the creation of a final image of the alignment. The service is named FASMA and is available at http： / /bioinformatica.isa.cnr.it /FASMA /.展开更多
[Objective] The molecular weight,isoelectric point,signal peptide,domain and other properties of the encoding protein of the known cystatin genes were analyzed.[Method] Cystatin genes were searched in NCBI and the rel...[Objective] The molecular weight,isoelectric point,signal peptide,domain and other properties of the encoding protein of the known cystatin genes were analyzed.[Method] Cystatin genes were searched in NCBI and the related amino acids sequences were downloaded.SMART software was used to predict the domain.SingalP program was used to search signal peptide.TMHMM program was used to search and predict the transmembrane domain.CLUSTAL W program was used to make multiple sequence alignment.Using MEGA3.1 software,...展开更多
A fundamental goal in cellular signaling is to understand allosteric communication, the process by which sig-nals originating at one site in a protein propagate reliably to affect distant functional sites. The general...A fundamental goal in cellular signaling is to understand allosteric communication, the process by which sig-nals originating at one site in a protein propagate reliably to affect distant functional sites. The general principles of protein structure that underlie this process remain unknown. Statistical coupling analysis （SCA） is a statistical technique that uses evolutionary data of a protein family to measure correlation between distant functional sites and suggests allosteric communication. In proteins, very distant and small interactions between collections of amino acids provide the communication which can be important for signaling process. In this paper, we present the SCA of protein alignment of the esterase family （pfam ID： PF00756） containing the sequence of antigen 85C secreted by Mycobacterium tuberculosis to identify a subset of interacting residues. Clustering analysis of the pairwise correlation highlighted seven important residue positions in the esterase family alignments. These resi-dues were then mapped on the crystal structure of antigen 85C （PDB ID： 1DQZ）. The mapping revealed corre-lation between 3 distant residues （Asp38, Leu123 and Met125） and suggests allosteric communication between them. This information can be used for a new drug against this fatal disease.展开更多
Soybean mosaic virus （SMV）, a member of the genus Potyvirus, is a major pathogen of soybean plants in China, and 16 SMV strains have been identified nationwide based on a former detailed SMV classification system. A...Soybean mosaic virus （SMV）, a member of the genus Potyvirus, is a major pathogen of soybean plants in China, and 16 SMV strains have been identified nationwide based on a former detailed SMV classification system. As the P3 gene is thought to be involved in viral replication, systemic infection, pathogenicity, and overcoming resistance, knowledge of the P3 gene sequences of SMV and other potyviruses would be useful in efforts to know the genetic relationships among them and control the disease. P3 gene sequences were obtained from representative isolates of the above-mentioned 16 SMV strains and were compared with other SMV strains and 16 Potyvirus species from the National Center for Biotechnology GenBank database. The P3 genes from the 16 SMV isolates are composed of 1041 nucleotides, encoding 347 amino acids, and share 90.7-100% nucleotide （NT） sequence identities and 95.1-100% amino acid （AA） sequence identities. The P3 coding regions of the 16 SMV isolates share high identities （92.4-98.9% NT and 96.0-100% AA） with the reported Korean isolates, followed by the USA isolates （88.5-97.9% NT and 91.4-98.6% AA）, and share low identities （80.5-85.2% NT and 82.1-84.7% AA） with the reported HZ 1 and P isolates from Pinellia ternata. The sequence identities of the P3 genes between SMV and the 16 potyviruses varied from 44.4 to 81.9% in the NT sequences and from 21.4 to 85.3% in the AA sequences, respectively. Among them, SMV was closely related to Watermelon mosaic virus （WMV）, with 76.0-81.9% NT and 77.5-85.3% AA identities. In addition, the SMV isolates and potyvirus species were clustered into six distinct groups. All the SMV strains isolated from soybean were clustered in Group I, and the remaining species were clustered in other groups. A multiple sequence alignment analysis of the C-terminal regions indicated that the P3 genes within a species were highly conserved, whereas those among species were relatively variable.展开更多
This article seeks to emphasize a simplified approach to phylogeny research using complete mitochondrial genomes alone, while touching upon a number of technological perspectives, such as algorithmic selection, which ...This article seeks to emphasize a simplified approach to phylogeny research using complete mitochondrial genomes alone, while touching upon a number of technological perspectives, such as algorithmic selection, which can help improve accuracy and performance in comparative analysis. My results will show that reliable estimations can be obtained by using mitochondrial markers, even among time-extended taxonomical rankings. Six distinct mammalian groups of taxa were selected for comparison. In all cases, mtDNA models generated reliable phylogeny approximations when compared against other independent data, while rendering exceptional computational performance.展开更多
There are many web-based multiple sequence alignment services accessible around the world. However, many researchers working on biological sequence analysis still struggle with inefficient, unfriendly user interface, ...There are many web-based multiple sequence alignment services accessible around the world. However, many researchers working on biological sequence analysis still struggle with inefficient, unfriendly user interface, and limited capability multiple sequence alignment software. In this study, we provide a comprehensive survey of regional and continental facilities that provide web-based alignment services. We also analyze and identify much needed services that are not available through these existing service providers. We then implement a web-based model to address these needs. From that perspective, our web-based multiple sequence alignment server, SeqAna, provides a unique set of services that none of these studied facilities have. For example, SeqAna provides a multiple sequence alignment scoring and ranking service. This service, the only of its kind, allows SeqAna＇s users to perform multiple sequence alignment with several alignment tools and rank the results of these alignments in the order of quality. With this service, SeqAna＇s users will be able to identify which alignment tools are more appropriate for their specific set of sequences. In addition, SeqAna＇s users can customize a small alignment sample as a reference for SeqAna to automatically identify the best tool to align their large set of sequences.展开更多
The recent explosion of biological data and the concomitant proliferation of distributed databases make it challenging for biologists and bioinformaticians to discover the best data resources for their needs, and the ...The recent explosion of biological data and the concomitant proliferation of distributed databases make it challenging for biologists and bioinformaticians to discover the best data resources for their needs, and the most efficient way to access and use them For the biologist, running bioinformatics analyses involve a time-consuming management of data and tools. Users need support to organize their work, retrieve parameters and reproduce their analyses. They also need to be able to combine their analytic tools using a safe data flow software mechanism. Finally we have designed a system, Bioinfo-Portal, to provide a flexible and usable web environment for defining and running bioinformatics analyses. It embeds simple yet powerful data management features that allow the user to reproduce analyses and to combine tools using an adobe flex tool. Bioinfo-Portal can also act as a front end to provide a unified view of already-existing collections of bioinformatics resources. Users can analyze genomic and proteomic data by using the tools that has been integrated in the portal （tools for alignments, dotplots, motif detection, domain analysis, profile searching and tertiary structure prediction）. The sequences that user obtained from portal＇s nucleotide and protein databases are easily analyzed by the portal tools on the same interface in no time. User can also take benefit from the animations.展开更多
文摘Multiple sequence alignments are successfully applied in many studies for understanding the structural and functional relations among single nucleic acids and protein sequences as well as whole families. Because of the rapid growth of sequence databases, multiple sequence alignments can often be very large and difficult to visualize and analyze. We offer a new service aimed to visualize and analyze the multiple alignments obtained with different external algorithms, with new features useful for the comparison of the aligned sequences as well as for the creation of a final image of the alignment. The service is named FASMA and is available at http： / /bioinformatica.isa.cnr.it /FASMA /.
文摘[Objective] The molecular weight,isoelectric point,signal peptide,domain and other properties of the encoding protein of the known cystatin genes were analyzed.[Method] Cystatin genes were searched in NCBI and the related amino acids sequences were downloaded.SMART software was used to predict the domain.SingalP program was used to search signal peptide.TMHMM program was used to search and predict the transmembrane domain.CLUSTAL W program was used to make multiple sequence alignment.Using MEGA3.1 software,...
文摘A fundamental goal in cellular signaling is to understand allosteric communication, the process by which sig-nals originating at one site in a protein propagate reliably to affect distant functional sites. The general principles of protein structure that underlie this process remain unknown. Statistical coupling analysis （SCA） is a statistical technique that uses evolutionary data of a protein family to measure correlation between distant functional sites and suggests allosteric communication. In proteins, very distant and small interactions between collections of amino acids provide the communication which can be important for signaling process. In this paper, we present the SCA of protein alignment of the esterase family （pfam ID： PF00756） containing the sequence of antigen 85C secreted by Mycobacterium tuberculosis to identify a subset of interacting residues. Clustering analysis of the pairwise correlation highlighted seven important residue positions in the esterase family alignments. These resi-dues were then mapped on the crystal structure of antigen 85C （PDB ID： 1DQZ）. The mapping revealed corre-lation between 3 distant residues （Asp38, Leu123 and Met125） and suggests allosteric communication between them. This information can be used for a new drug against this fatal disease.
基金supported by the National Natural Science Foundation of China(30671266,31101164)the National Basic Research Program of China(2006CB101708,2009CB118404)+2 种基金the National 863 Program of China(2006AA100104)the 111 Project from Ministry of Education of China(B08025)the Youth Science and Technology Innovation Foundation of Nanjing Agriculture University,China(KJ2010002)
文摘Soybean mosaic virus （SMV）, a member of the genus Potyvirus, is a major pathogen of soybean plants in China, and 16 SMV strains have been identified nationwide based on a former detailed SMV classification system. As the P3 gene is thought to be involved in viral replication, systemic infection, pathogenicity, and overcoming resistance, knowledge of the P3 gene sequences of SMV and other potyviruses would be useful in efforts to know the genetic relationships among them and control the disease. P3 gene sequences were obtained from representative isolates of the above-mentioned 16 SMV strains and were compared with other SMV strains and 16 Potyvirus species from the National Center for Biotechnology GenBank database. The P3 genes from the 16 SMV isolates are composed of 1041 nucleotides, encoding 347 amino acids, and share 90.7-100% nucleotide （NT） sequence identities and 95.1-100% amino acid （AA） sequence identities. The P3 coding regions of the 16 SMV isolates share high identities （92.4-98.9% NT and 96.0-100% AA） with the reported Korean isolates, followed by the USA isolates （88.5-97.9% NT and 91.4-98.6% AA）, and share low identities （80.5-85.2% NT and 82.1-84.7% AA） with the reported HZ 1 and P isolates from Pinellia ternata. The sequence identities of the P3 genes between SMV and the 16 potyviruses varied from 44.4 to 81.9% in the NT sequences and from 21.4 to 85.3% in the AA sequences, respectively. Among them, SMV was closely related to Watermelon mosaic virus （WMV）, with 76.0-81.9% NT and 77.5-85.3% AA identities. In addition, the SMV isolates and potyvirus species were clustered into six distinct groups. All the SMV strains isolated from soybean were clustered in Group I, and the remaining species were clustered in other groups. A multiple sequence alignment analysis of the C-terminal regions indicated that the P3 genes within a species were highly conserved, whereas those among species were relatively variable.
文摘This article seeks to emphasize a simplified approach to phylogeny research using complete mitochondrial genomes alone, while touching upon a number of technological perspectives, such as algorithmic selection, which can help improve accuracy and performance in comparative analysis. My results will show that reliable estimations can be obtained by using mitochondrial markers, even among time-extended taxonomical rankings. Six distinct mammalian groups of taxa were selected for comparison. In all cases, mtDNA models generated reliable phylogeny approximations when compared against other independent data, while rendering exceptional computational performance.
文摘There are many web-based multiple sequence alignment services accessible around the world. However, many researchers working on biological sequence analysis still struggle with inefficient, unfriendly user interface, and limited capability multiple sequence alignment software. In this study, we provide a comprehensive survey of regional and continental facilities that provide web-based alignment services. We also analyze and identify much needed services that are not available through these existing service providers. We then implement a web-based model to address these needs. From that perspective, our web-based multiple sequence alignment server, SeqAna, provides a unique set of services that none of these studied facilities have. For example, SeqAna provides a multiple sequence alignment scoring and ranking service. This service, the only of its kind, allows SeqAna＇s users to perform multiple sequence alignment with several alignment tools and rank the results of these alignments in the order of quality. With this service, SeqAna＇s users will be able to identify which alignment tools are more appropriate for their specific set of sequences. In addition, SeqAna＇s users can customize a small alignment sample as a reference for SeqAna to automatically identify the best tool to align their large set of sequences.
文摘The recent explosion of biological data and the concomitant proliferation of distributed databases make it challenging for biologists and bioinformaticians to discover the best data resources for their needs, and the most efficient way to access and use them For the biologist, running bioinformatics analyses involve a time-consuming management of data and tools. Users need support to organize their work, retrieve parameters and reproduce their analyses. They also need to be able to combine their analytic tools using a safe data flow software mechanism. Finally we have designed a system, Bioinfo-Portal, to provide a flexible and usable web environment for defining and running bioinformatics analyses. It embeds simple yet powerful data management features that allow the user to reproduce analyses and to combine tools using an adobe flex tool. Bioinfo-Portal can also act as a front end to provide a unified view of already-existing collections of bioinformatics resources. Users can analyze genomic and proteomic data by using the tools that has been integrated in the portal （tools for alignments, dotplots, motif detection, domain analysis, profile searching and tertiary structure prediction）. The sequences that user obtained from portal＇s nucleotide and protein databases are easily analyzed by the portal tools on the same interface in no time. User can also take benefit from the animations.
