PSI-BLAST swMATH ID: 17324 Software Authors: Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.J. Description: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSIBLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily. Homepage: http://nar.oxfordjournals.org/content/25/17/3389.short Related Software: BLAST; Pfam; UniProt; ClustalW; MUSCLE; LIBSVM; Cell-PLoc; Cd-hit; KEGG; iRSpot-PseDNC; PROSITE; MODELLER; iLoc-Euk; iLoc-Virus; AAindex; BLAT; pSuc-Lys; EMBOSS; COMPASS; DIALIGN Cited in: 140 Publications all top 5 Cited by 388 Authors 4 Dehzangi, Abdollah 4 Di Giulio, Massimo 4 Sharma, Alok 3 Abboud, Amir 3 Liang, Yunyun 3 Mei, Suyu 3 Mondal, Sukanta 3 Zhang, Shengli 2 Amani, Jafar 2 Araabi, Babak Nadjar 2 Bonatto, Diego 2 Cai, Yudong 2 Carbone, Alessandra 2 Dai, Qi 2 Du, Pufeng 2 Fattahian, Yaser 2 Gargari, Seyed Latif Mousavi 2 Gullotto, Danilo 2 Jiao, Ya-Sen 2 Kavousi, Kaveh 2 Li, Menglong 2 Li, Yixue 2 Liu, Xiaoqing 2 Lyons, James E. 2 Mahapatra, Rajani Kanta 2 Moosavi-Movahedi, Ali Akbar 2 Moshiri, Behzad 2 Oehmen, Christopher S. 2 Pai, Priyadarshini P. 2 Paliwal, Kuldip K. 2 Qi, Zhaohui 2 Rahbar, Mohammad Reza 2 Rasooli, Iraj 2 Sadeghi, Mehdi 2 Seligmann, Hervé 2 Spouge, John L. 2 Webb-Robertson, Bobbie-Jo M. 1 Acharya, Tinku 1 Agarwal, Shivani 1 Agüero-Chapin, Guillermin 1 Aguilar-Ruiz, Jesus Salvador 1 Ahmad, Jamal 1 Aita, Takuyo 1 Akindahunsi, Akintunde A. 1 Alexov, Emil 1 Aluru, Srinivas 1 Amir-Ghiasvand, Farid 1 Amoutzias, Grigoris 1 Antunes, Agostinho 1 Arampatzidou, Maria 1 Araújo, D. A. M. 1 Archetti, Marco 1 Arzberger, Peter W. 1 Asencio-Cortes, Gualberto 1 Atalay, Volkan 1 Atchley, William R. 1 Athitsos, Vassilis 1 Axelson-Fisk, Marina 1 Bačkurs, Artūrs 1 Bandiera, Antonella 1 Bao, Chaohui 1 Barea, Fernanda 1 Barker, Winona C. 1 Barreto, George E. 1 Barth, Dominique 1 Basak, Jolly 1 Berkemer, Sarah J. 1 Bernini, Andrea 1 Bhavna, Rajasekaran 1 Biswas, Neela 1 Błażewicz, Jacek 1 Blockeel, Hendrik 1 Bolshoy, Alexander 1 Borneman, James 1 Brendel, Martin 1 Bringmann, Karl 1 Cao, Wei 1 Cao, Zhiwei 1 Capani, Francisco 1 Cesa-Bianchi, Nicolò 1 Cetin-Atalay, Rengul 1 Chakrabarti, Arunabha 1 Chakrabarti, Chaitali 1 Chang, Ming-Shi 1 Charikar, Moses S. 1 Chen, Ruoying 1 Chen, Shu-An 1 Chen, Wei 1 Cheung, Yiuming 1 Cohen, Johanne 1 Collado-Vides, Julio 1 Comet, Jean-Paul 1 Coull, Scott E. 1 Cui, Xinping 1 Das, Gautam Kumar 1 Dash, Tirtharaj 1 de Brevern, Alexandre G. 1 de la Riva, Gustavo Alberto 1 Dea-Ayuela, María A. 1 Denise, Alain ...and 288 more Authors all top 5 Cited in 39 Serials 55 Journal of Theoretical Biology 24 Computational Biology and Chemistry 3 Mathematical Biosciences 3 Physica A 3 Journal of Computer and System Sciences 3 Theoretical Computer Science 3 Machine Learning 3 Computational Statistics and Data Analysis 2 Journal of Computational Physics 2 Pattern Recognition 2 Data Mining and Knowledge Discovery 2 Statistical Applications in Genetics and Molecular Biology 2 Mathematics in Computer Science 2 1 Discrete Applied Mathematics 1 Journal of Mathematical Analysis and Applications 1 Journal of Mathematical Biology 1 Bulletin of Mathematical Biology 1 The Annals of Statistics 1 Information Sciences 1 Nonlinear Analysis. Theory, Methods & Applications. Series A: Theory and Methods 1 Theoretical Population Biology 1 Parallel Computing 1 New Generation Computing 1 Journal of Parallel and Distributed Computing 1 Annals of Operations Research 1 Journal of Logic and Computation 1 Computational Optimization and Applications 1 Journal of Mathematical Chemistry 1 PAA. Pattern Analysis and Applications 1 Journal of Applied Statistics 1 Extremes 1 Journal of Discrete Algorithms 1 Computational & Mathematical Methods in Medicine 1 Communications in Computational Physics 1 Statistical Analysis and Data Mining 1 Computational Biology 1 Chapman & Hall/CRC Computer and Information Science Series 1 Methods in Molecular Biology all top 5 Cited in 16 Fields 118 Biology and other natural sciences (92-XX) 45 Computer science (68-XX) 24 Statistics (62-XX) 11 Operations research, mathematical programming (90-XX) 5 Combinatorics (05-XX) 3 Probability theory and stochastic processes (60-XX) 2 Number theory (11-XX) 2 Numerical analysis (65-XX) 1 General and overarching topics; collections (00-XX) 1 Mathematical logic and foundations (03-XX) 1 Measure and integration (28-XX) 1 Functional analysis (46-XX) 1 Statistical mechanics, structure of matter (82-XX) 1 Game theory, economics, finance, and other social and behavioral sciences (91-XX) 1 Systems theory; control (93-XX) 1 Information and communication theory, circuits (94-XX) Citations by Year