The bioinformatics in Vietnamese academic education. Software resources, reliability and development

• Autorzy: Leluk J.
• Języki publikacji: EN

Abstrakty

EN

Since 2005 the education program at bioinformatics an molecular modeling is being developed in Vietnam national universities with the cooperation of the University of Zielona Góra (Poland). This program requires good support concerning the biological databases and bioinformatics software. A number of good quality and comprehensive genomic an protein sequence databases and protein structure database are freely accessible online for academic use and scientific research. Also there are accessible the specialized genomic databases kindly provided by Human Genome Center at Tokyo University. Similar situation concerns the bioinformatics software. However the quality and reliability of the accessible software is not always very good. Therefore the Polish group cooperating with the Vietnam National University has elaborated and supplied the academic community in Vietnam with the new and original applications. They replenish the current needs of the users studying bioinformatics and raise the quality of the obtained results. The original applications which enrich the VNU bioinformastics resources (an are solely available only in bioinformatics centers in Hanoi and Poland) are: GEISHA - a nonstatistic application for sequence multiple alignment based on genetic semihomology algorithm. Corm - application for locating and analysing the intramolecular correlated mutations. Consensus Constructor - program for consensus sequence construction. SSSS - program for sequence similarity significance estimation. Talana - protein variability/conservativity analyzer and visualiser. Nitano - detection of intra- and intermolecular residue colocations, protein contact map creator. Keram - program to detect and analyze correlated mutations.v Retamgar - calculator of 2D, 3D, 4D points distance within a protein molecule. Cylanu - PDB file modifier. SecMaker - random protein sequence generator. Byrnik - program for sequence comparison. MMCC - molecule mass centre calculator. Hypro - protein hydrophobicity profiler. These resources contributed in the formation of the first academic Bioinformatics Center in this region of Asia, located at Hanoi University of Science. Within two last years the cooperation has been developed and extended by the long term study program for Vinh University students at University of Zielona Góra. At present two other universities joined the cooperation - Hanoi University of Agriculture and International University of HCMC. In all cases the bioinformatics and molecular modeling play the leading role in both educational and scientific activity.

Słowa kluczowe

EN

e-learning; education; bioinformatics software; software reliability; Vietnam universities

• Wydawca: Uniwersytet Jagielloński - Collegium Medicum ; Index Copernicus Sp. z o.o.
• Czasopismo: Bio-Algorithms and Med-Systems
• Rocznik: 2010
• Tom: Vol. 6, no. 12
• Strony: 99--104
• Opis fizyczny: Bibliogr. 21 poz.

Twórcy

autor

Leluk J.

• Faculty of Biological Sciences, University of Zielona Góra, Poland

Bibliografia

• [1] Leluk J.: E-learning - the past, present and future perspectives, International Conference Hanoi Forum on Information-Communication Technology (ICT), 5-7.12.2007 Hanoi, Vietnam, Abstracts, 2007.
• [2] Berman H. M., Westbrook J., Feng Z., Gilliland G.,. Bhat T. N, Weissig H., Shindyalov I. N., Bourne P. E.: The Protein Data Bank, Nucl. Acids Res. 28: 235-242, 2000.
• [3] Berman H. M., Henrick K., Nakamura H.: Announcing the worldwide Protein Data Bank, Nature Structural Biology 10: 980, 2003.
• [4] Bernstein F. C., Koetzle T. F., Williams G. J. B., Meyer Jr E. F., Brice M. D., Rodgers J. R., Kennard O., Shimanouchi T., Tasumi M.: The Protein Data Bank: a computer-based archival file for macromolecular structures, J. Mol. Biol. 112: 535-542, 1997).
• [5] Suzuki Y., Yamashita R., Nakai K., Sugano S.: DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs, Nucl. Acids Res. 30: 328-331, 2002.
• [6] Suzuki Y., Yamashita R., Sugano S., Nakai K.: DBTSS, DataBase of Transcriptional Start Sites: progress report 2004, Nucl. Acids Res. 32, 2004.
• [7] Ishii T., Yoshida K., Terai G., Fujita Y., Nakai K.: DBTBS: a database of Bacillus subtilis promoters and transcription factors, Nucl. Acids Res. 29: 278-80, 2001.
• [8] Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J.: Basic local alignment search tool, J. Mol. Biol. 215: 403-410, 1990.
• [9] Leluk J.: A new algorithm for analysis of the homology in protein primary structure, Computers & Chemistry, 22: 123-131, 1998.
• [10] Leluk J.: A non-statistical approach to protein mutational variability, BioSystems, 56: 83-93, 2000.
• [11] Leluk J.: Regularities in mutational variability in selected protein families and the Markovian model of amino acid replacement, Computers & Chemistry, 24: 659-672, 2000.
• [12] Leluk J., Hanus-Lorenz B., Sikorski A. F.: Application of genetic semihomology algorithm to theoretical studies on various protein families, Acta Biochim. Polon. 48: 21-33, 2001.
• [13] Górecki A., Leluk J., Lesyng B.: A Java-implementation of a genetic semihomology algorithm (GEISHA), and its applications for analyses of selected protein families, 29th FEBS Congress, 26 June - 1 July 2004, Warsaw, POLAND, Eur. J. Biochem., 271, Supplement, 30, 2004.
• [14] Kuśka J., Leluk J., Lesyng B.: Novel analysis of correlated mutations in kinases and its potential applications, Bioinformatics 2008 Conference, 24-27 April, 2008 Warsaw, Poland, Abstracts: 45, 2008.
• [15] Fogtman A., Leluk J., Lesyng B.: β-Spectrin consensus sequence construction with variable threshold parameters; verification of their usefulness, The International Conference Sequence-Structure-Function Relationships; Theoretical and Experimental Approaches, Warsaw, Poland, April 6-10 2005, Abstracts: 12, 2005.
• [16] Leluk J., Mikołajczyk A.: A new approach to sequence comparison and similarity estimation, 29th FEBS Congress, 26 June - 1 July 2004, Warsaw, POLAND, Eur. J. Biochem., 271, Supplement: 29, 2004.
• [17] Gajewska E., Leluk J.: An Approach to Sequence Similarity Significance Estimation, Bio-Algorithms and Med-Systems (ed. Medical College, Jagiellonian University), 1: 121-124, 2005.
• [18] Kuśka J., Leluk J.: BIOW@RE: A package of applications for intra/intermolecular interaction studies, 5th International Conference "Inhibitors of Protein Kinases", Acta Biochim. Polon., 54 (Supplement 3): 61-62, 2007.
• [19] Neher E.: How frequent are correlated changes in families of protein sequences, Proc. Natl. Acad. Sci. USA 91: 98-102, 1993.
• [20] Oliveira L., Pavia A. C. M., Vriend G.: Correlated Mutation Analyses on Very Large Sequence Families, Chembiochem. 3(10): 1010-1017, 2002.
• [21] George D. G., Barker W. C., Hunt L. T: Mutation data matrix and its uses. In: Doolittle, R. F., (Ed.) Methods in Enzymology, Academic Press, San Diego, CA, 183: 337, 1990.