RANDOMBLAST A TOOL TO GENERATE RANDOM “NEVER BORN PROTEIN” SEQUENCES
作者： Pier Luigi Luisi , Fabio Polticelli , Giovanni Minervini , Giuseppe Evangelista
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摘要: Abstract : In an accompanying paper by Minervini et al., we deal with the scientific problem of studying sequence to structure relationships in “never born proteins” (NBPs), i.e. protein sequences which have never been observed nature. The study structural and functional properties "never proteins" requires generation a large library characterized absence any significant similarity all known sequences. this describe implementation simple command-line software utility used generate random amino acid filter them against NCBI non redundant database, using as threshold value Evalue parameter returned well comparison Blast. This utility, named RandomBlast, has written C programming language for Windows operating systems. implications NBPs composition are discussed compared natural proteins comparable length.
参考文章(8)
Carol A Rohl, Charlie EM Strauss, Kira MS Misura, David Baker, None, Protein structure prediction using Rosetta. Methods in Enzymology. ,vol. 383, pp. 66- 93 ,(2004) , 10.1016/S0076-6879(04)83004-0
Cristiano Chiarabelli, Jan W. Vrijbloed, Davide De Lucrezia, Richard M. Thomas, Pasquale Stano, Fabio Polticelli, Tiziana Ottone, Ester Papa, Pier Luigi Luisi, Investigation of de novo totally random biosequences, Part II: On the folding frequency in a totally random library of de novo proteins obtained by phage display. Chemistry & Biodiversity. ,vol. 3, pp. 840- 859 ,(2006) , 10.1002/CBDV.200690088
Fredj Tekaia, Edouard Yeramian, Bernard Dujon, Amino acid composition of genomes, lifestyles of organisms, and evolutionary trends: a global picture with correspondence analysis Gene. ,vol. 297, pp. 51- 60 ,(2002) , 10.1016/S0378-1119(02)00871-5
S Altschula, Warren Gisha, Webb Millerb, E Meyersc, D Lipmana, None, Basic Local Alignment Search Tool Journal of Molecular Biology. ,vol. 215, pp. 403- 410 ,(1990) , 10.1016/S0022-2836(05)80360-2
S. Karlin, S. F. Altschul, Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes Proceedings of the National Academy of Sciences of the United States of America. ,vol. 87, pp. 2264- 2268 ,(1990) , 10.1073/PNAS.87.6.2264
Makoto Matsumoto, Takuji Nishimura, Mersenne twister: a 623-dimensionally equidistributed uniform pseudo-random number generator ACM Transactions on Modeling and Computer Simulation. ,vol. 8, pp. 3- 30 ,(1998) , 10.1145/272991.272995
David L Wheeler, Deanna M Church, Ron Edgar, Scott Federhen, Wolfgang Helmberg, Thomas L Madden, Joan U Pontius, Gregory D Schuler, Lynn M Schriml, Edwin Sequeira, Tugba O Suzek, Tatiana A Tatusova, Lukas Wagner, None, Database resources of the National Center for Biotechnology Information: update Nucleic Acids Research. ,vol. 32, pp. 35D- 40 ,(2004) , 10.1093/NAR/GKH073
Amos Bairoch, Brigitte Boeckmann, Serenella Ferro, Elisabeth Gasteiger, Swiss-Prot: Juggling between evolution and stability Briefings in Bioinformatics. ,vol. 5, pp. 39- 55 ,(2004) , 10.1093/BIB/5.1.39