检索结果-南通市图书馆

Genomics, Proteomics & Bioinformatics 2010年第2期8卷 127-134页

作者： Jayavel Sridhar Govindaraj Sowmiya kanagaraj sekar Ziauddin Ahamed Rafi Centre of Excellence in Bioinformatics School of BiotechnologyMadurai Kamaraj University Bioinformatics Centre Indian Institute of Science Supercomputer Education and Research Centre Indian Institute of Science

Small RNAs （sRNAs） are non-coding transcripts exerting their functions in the cells directly. Identification of sRNAs is a difficult task due to the lack of clear sequence and structural biases. Most sRNAs are identified within genus specific intergenic regions in related genomes. However, several of these regions remain un-annotated due to lack of sequence homology and/or potent statistical identification tools. A computational engine has been built to search within the intergenic regions to identify and roughly annotate new putative sRNA regions in Enterobacteriaceae genomes. It utilizes experimentally known sRNA data and their flanking genes/KEGG Orthology （KO） numbers as templates to identify similar sRNA regions in related query genomes. The search engine not only has the capability to locate putative intergenic regions for specific sRNAs, but also has the potency to locate conserved, shuffled or deleted gene clusters in query genomes. Because it uses the KO terms for locating functionally important regions such as sRNAs, any further KO number assignment to additional genes will increase the sensitivity. The PsRNA server is used for the identification of putative sRNA regions through the information retrieved from the sRNA of interest. The computing engine is available online at http：//bioserver 1 .***/psrna/and http：//***： 8081/psrna/.

关键词： small RNA KEGG Orthology flanking genes intergenic regions

SMS 2.0: An Updated Database to Study the Structural Plasticity of Short Peptide Fragments in Non-redundant Proteins

在线全文

学校读者我要写书评

暂无评论

Genomics, Proteomics & Bioinformatics 2012年第1期10卷 44-50页

作者： Dheeraj Ravella Muthukumarasamy Uthaya Kumar Durairaj Sherlin Mani Shankar Marthandan Kirti Vaishnavi kanagaraj sekar Bioinformatics Centre (Centre of Excellence in Structural Biology and Bio-computing) Supercomputer Education and Research Centre Indian Institute of Science Bangalore 560012 India

The function of a protein molecule is greatly influenced by its three-dimensional （3D） structure and therefore structure prediction will help identify its biological function. We have updated Sequence, Motif and Structure （SMS）, the database of structurally rigid peptide fragments, by combining amino acid sequences and the corre- sponding 3D atomic coordinates of non-redundant （25%） and redundant （90%） protein chains available in the Protein Data Bank （PDB）. SMS 2.0 provides information pertaining to the peptide fragments of length 5-14 resi- dues. The entire dataset is divided into three categories, namely, same sequence motifs having similar, intermedi- ate or dissimilar 3D structures. Further, options are provided to facilitate structural superposition using the pro- gram structural alignment of multiple proteins （STAMP） and the popular JAVA plug-in （Jmol） is deployed for visualization. In addition, functionalities are provided to search for the occurrences of the sequence motifs in other structural and sequence databases like PDB, Genome Database （GDB）, Protein Information Resource （PIR） and Swiss-Prot. The updated database along with the search engine is available over the World Wide Web through the following URL http：//***/sms/.

关键词： non-redundant protein chains sequence motifs 3D structure structural superposition

Junker: An Intergenic Explorer for Bacterial Genomes

在线全文

学校读者我要写书评

暂无评论

Genomics, Proteomics & Bioinformatics 2011年第4期9卷 179-182页

作者： Jayavel Sridhar Radhakrishnan Sabarinathan Shanmugam Siva Balan Ziauddin Ahamed Rafi Paramasamy Gunasekaran kanagaraj sekar Centre of Excellence in Bioinformatics School of Biotechnology Madurai Kamaraj University UGC-Networking Resource Centre in Biological Sciences School of Biological Sciences Madurai Kamaraj University Bioinformatics Centre Indian Institute of Science

In the past few decades, scientists from all over the world have taken a keen interest in novel functional units such as small regulatory RNAs, small open reading frames, pseudogenes, transposons, integrase binding attB/attP sites, repeat elements within the bacterial intergenic regions （IGRs） and in the analysis of those ＂junk＂ regions for ge- nomic complexity. Here we have developed a web server, named Junker, to facilitate the in-depth analysis of IGRs for examining their length distribution, four-quadrant plots, GC percentage and repeat details. Upon selection of a particular bacterial genome, the physical genome map is displayed as a multiple loci with options to view any loci of interest in detail. In addition, an IGR statistics module has been created and implemented in the web server to analyze the length distribution of the IGRs and to understand the disordered grouping of IGRs across the genome by generating the four-quadrant plots. The proposed web server is freely available at the URL http：//***/junker/.

关键词： bacterial genome intergenic region web server statistics module

Homepeptide Repeats:Implications for Protein Structure,Function and Evolution

在线全文

学校读者我要写书评

暂无评论

Genomics, Proteomics & Bioinformatics 2012年第4期10卷 217-225页

作者： Muthukumarasamy Uthayakumar Bowdadu Benazir Sanjeev Patra Marthandan Kirti Vaishnavi Manickam Gurusaran kanagarajan Sureka Jeyaraman Jeyakanthan kanagaraj sekar Supercomputer Education and Research Centre Indian Institute of ScienceBangalore 560012India Department of Bioinformatics Alagappa UniversityKaraikudi 630003India

Analysis of protein sequences from Mycobacterium tuberculosis H37Rv （Mtb H37Rv） was performed to identify homopeptide repeat- containing proteins （HRCPs）. Functional annotation of the HRCPs showed that they are preferentially involved in cellular metabolism. Furthermore, these homopeptide repeats might play some specific roles in protein-protein interaction. Repeat length differences among Bacteria, Archaea and Eukaryotes were calculated in order to identify the conservation of the repeats in these divergent kingdoms. From the results, it was evident that these repeats have a higher degree of conservation in Bacteria and Archaea than in Eukaryotes. In addi- tion, there seems to be a direct correlation between the repeat length difference and the degree of divergence between the species. Our study supports the hypothesis that the presence of homopeptide repeats influences the rate of evolution of the protein sequences in which they are embedded. Thus, homopeptide repeat may have structural, functional and evolutionary implications on proteins.

关键词： Homopeptide repeats Disordered regions Replication slippage Protein domains Rate of evolution