title: SOSUI-GramN: high performance prediction for sub-cellular localization of proteins in gram-negative bacteria.
abstract: A predictive software system, SOSUI-GramN, was developed for assessing the subcellular localization of proteins in Gram-negative bacteria. The system does not require the sequence homology data of any known sequences; instead, it uses only physicochemical parameters of the N- and C-terminal signal sequences, and the total sequence. The precision of the prediction system for subcellular localization to extracellular, outer membrane, periplasm, inner membrane and cytoplasmic medium was 92.3%, 89.4%, 86.4%, 97.5% and 93.5%, respectively, with corresponding recall rates of 70.3%, 87.5%, 76.0%, 97.5% and 88.4%, respectively. The overall performance for precision and recall obtained using this method was 92.9% and 86.7%, respectively. The comparison of performance of SOSUI-GramN with that of other methods showed the performance of prediction for extracellular proteins, as well as inner and outer membrane proteins, was either superior or equivalent to that obtained with other systems. SOSUI-GramN particularly improved the accuracy for predictions of extracellular proteins which is an area of weakness common to the other methods.
authors.affiliation: Department of Applied Physics, Graduate School of Engineering, Nagoya University, Furocho, Chikusa-ku, Nagoya 464-8606, Japan. imai@bp.nuap.nagoya-u.ac.jp
authors.forename: Kenichiro
authors.initials: K
authors.lastname: Imai
authors.forename: Naoyuki
authors.initials: N
authors.lastname: Asakawa
authors.forename: Toshiyuki
authors.initials: T
authors.lastname: Tsuji
authors.forename: Fumitsugu
authors.initials: F
authors.lastname: Akazawa
authors.forename: Ayano
authors.initials: A
authors.lastname: Ino
authors.forename: Masashi
authors.initials: M
authors.lastname: Sonoyama
authors.forename: Shigeki
authors.initials: S
authors.lastname: Mitaku
references.citation: Proteins. 2006 Aug 15;64(3):643-51
references.pmid: 16752418
references.citation: Nat Rev Microbiol. 2006 Oct;4(10):741-51
references.pmid: 16964270
references.citation: Bioinformatics. 2002 Apr;18(4):608-16
references.pmid: 12016058
references.citation: J Mol Biol. 1982 May 5;157(1):105-32
references.pmid: 7108955
references.citation: Int J Med Microbiol. 2007 Oct;297(6):401-15
references.pmid: 17482513
references.citation: Bioinformatics. 2005 Mar 1;21(5):617-23
references.pmid: 15501914
references.citation: Bioinformatics. 2005 May 15;21(10):2522-4
references.pmid: 15699023
references.citation: Bioinformatics. 1998;14(4):378-9
references.pmid: 9632836
references.citation: Nucleic Acids Res. 2005 Jan 1;33(Database issue):D164-8
references.pmid: 15608169
references.citation: J Bacteriol. 2005 Jul;187(13):4306-14
references.pmid: 15968039
references.citation: BMC Bioinformatics. 2005 Jul 13;6:174
references.pmid: 16011808