Automatic prediction of protein function, Cell Mol Life Sci, vol.60, issue.12, pp.2637-2650, 2003. ,
Identification and correction of abnormal, incomplete and mispredicted proteins in public databases, BMC Bioinformatics, vol.9, issue.1, p.353, 2008. ,
DOI : 10.1186/1471-2105-9-353
Secretion and subcellular localizations of bacterial proteins: a semantic awareness issue, Trends in Microbiology, vol.17, issue.4, pp.139-145, 2009. ,
DOI : 10.1016/j.tim.2009.01.004
Root-microbe communication through protein secretion. The Journal of biological chemistry, pp.25247-25255, 2008. ,
Evidence that protein constituents of postsynaptic membrane specializations are locally synthesized: Time course of appearance of recently synthesized proteins in synaptic junctions, Journal of Neuroscience Research, vol.101, issue.4, pp.649-660, 1991. ,
DOI : 10.1002/jnr.490300408
Proteins Exported via the PrsD-PrsE Type I Secretion System and the Acidic Exopolysaccharide Are Involved in Biofilm Formation by Rhizobium leguminosarum, Journal of Bacteriology, vol.188, issue.12, pp.1884474-4486, 2006. ,
DOI : 10.1128/JB.00246-06
Pleiotropic effects of the twin-arginine translocation system on biofilm formation, colonization, and virulence in Vibrio cholerae, BMC Microbiology, vol.9, issue.1, p.114, 2009. ,
DOI : 10.1186/1471-2180-9-114
The role of protein secretion systems in the virulence of the intracellular pathogen Legionella pneumophila, Microbiology, vol.153, issue.12, pp.3948-3953, 2007. ,
DOI : 10.1099/mic.0.2007/012039-0
Secreted proteins from Ralstonia solanacearum: a hundred tricks to kill a plant, Current Opinion in Microbiology, vol.12, issue.1, pp.44-52, 2009. ,
DOI : 10.1016/j.mib.2008.11.008
Virulence factor secretion and translocation by Bordetella species. Current opinion in microbiology, pp.88-93, 2009. ,
Sec- and Tat-mediated protein secretion across the bacterial cytoplasmic membrane???Distinct translocases and mechanisms, Biochimica et Biophysica Acta (BBA) - Biomembranes, vol.1778, issue.9, pp.17781735-1756, 2008. ,
DOI : 10.1016/j.bbamem.2007.07.015
Bacterial protein secretion through the translocase nanomachine, Nature Reviews Microbiology, vol.363, issue.11, pp.839-851, 2007. ,
DOI : 10.1038/nrmicro1771
Twin-arginine-specific protein export in Escherichia coli, Research in microbiology 2005, pp.131-136 ,
DOI : 10.1016/j.resmic.2004.09.016
The bacterial twin-arginine translocation pathway. Annual review of microbiology, pp.373-395, 2006. ,
Protein secretion in the Archaea: multiple paths towards a unique cell surface, Nature Reviews Microbiology, vol.438, issue.7, pp.537-547, 2006. ,
DOI : 10.1038/nrmicro1440
The general secretory pathway: a general misnomer? Trends in microbiology, pp.306-309, 2004. ,
Type 1 protein secretion in bacteria, the ABC-transporter dependent pathway (review) Molecular membrane biology, pp.29-39, 2005. ,
Protein delivery into eukaryotic cells by type III secretion machines, Nature, vol.281, issue.7119, pp.567-573, 2006. ,
DOI : 10.1038/nature05272
Process of Protein Transport by the Type III Secretion System, Microbiology and Molecular Biology Reviews, vol.68, issue.4, pp.771-795, 2004. ,
DOI : 10.1128/MMBR.68.4.771-795.2004
Protein Homology Network Families Reveal Step-Wise Diversification of Type III and Type IV Secretion Systems, PLoS Computational Biology, vol.340, issue.12, p.173, 2006. ,
DOI : 10.1371/journal.pcbi.0020173.st005
The type VI secretion system: translocation of effectors and effector-domains. Current opinion in microbiology, pp.11-17, 2009. ,
The bacterial type VI secretion machine: yet another player for protein transport across membranes, Microbiology, vol.154, issue.6, pp.1570-1583, 2008. ,
DOI : 10.1099/mic.0.2008/016840-0
Type III secretion: what's in a name? Trends in microbiology, pp.157-160, 2006. ,
A new way out: protein localization on the bacterial cell surface via Tat and a novel Type II secretion system, Molecular Microbiology, vol.4, issue.6, pp.1331-1335, 2008. ,
DOI : 10.1111/j.1365-2958.2008.06367.x
Type II secretion: a protein secretion system for all seasons, Trends in Microbiology, vol.13, issue.12, pp.581-588, 2005. ,
DOI : 10.1016/j.tim.2005.09.005
The type III secretion system tip complex and translocon. Molecular microbiology, pp.1085-1095, 2008. ,
Type V Protein Secretion Pathway: the Autotransporter Story, Microbiology and Molecular Biology Reviews, vol.68, issue.4, pp.692-744, 2004. ,
DOI : 10.1128/MMBR.68.4.692-744.2004
Type V protein secretion: simplicity gone awry? Current issues in molecular biology, pp.111-124, 2004. ,
Evolution of the Chaperone/Usher Assembly Pathway: Fimbrial Classification Goes Greek, Microbiology and Molecular Biology Reviews, vol.71, issue.4, pp.551-575, 2007. ,
DOI : 10.1128/MMBR.00014-07
Fiber assembly by the chaperone???usher pathway, Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, vol.1694, issue.1-3, pp.259-267, 2004. ,
DOI : 10.1016/j.bbamcr.2004.02.010
Mechanisms of Protein Export across the Bacterial Outer Membrane, Journal of Bacteriology, vol.187, issue.13, pp.4306-4314, 2005. ,
DOI : 10.1128/JB.187.13.4306-4314.2005
Type VII secretion in mycobacteria: classification in line with cell envelope structure, Trends in Microbiology, vol.17, issue.8, pp.337-338, 2009. ,
DOI : 10.1016/j.tim.2009.05.007
Genomic analysis of the protein secretion systems in Clostridium acetobutylicum ATCC 824, Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, vol.1745, issue.2, pp.1745223-253, 2005. ,
DOI : 10.1016/j.bbamcr.2005.04.006
Type II protein secretion and its relationship to bacterial type IV pili and archaeal flagella, Microbiology, vol.149, issue.11, pp.1493051-3072, 2003. ,
DOI : 10.1099/mic.0.26364-0
How and when are substrates selected for type III secretion? Trends in microbiology, pp.209-214, 2001. ,
The ESAT-6/WXG100 superfamily ? and a new Gram-positive secretion system? Trends in microbiology, pp.209-212, 2002. ,
Outer membrane translocation: numerical protein secretion nomenclature in question in mycobacteria, Trends in Microbiology, vol.17, issue.8, pp.338-340, 2009. ,
DOI : 10.1016/j.tim.2009.05.008
Patterns of amino acids near signal-sequence cleavage sites. European journal of biochemistry/FEBS 1983, pp.17-21 ,
A new method for predicting signal sequence cleavage sites. Nucleic acids research, pp.4683-4690, 1986. ,
On the predictive recognition of signal peptide sequences. Virus research, pp.271-286, 1985. ,
Improving signal peptide prediction accuracy by simulated neural network, Bioinformatics, vol.7, issue.4, pp.485-487, 1991. ,
DOI : 10.1093/bioinformatics/7.4.485
Analysis of cleavage-site patterns in protein precursor sequences with a perceptron-type neural network. Biochemical and biophysical research communications, pp.951-959, 1993. ,
Prediction of signal peptides in protein sequences by neural networks, Acta biochimica Polonica, vol.55, issue.2, pp.261-267, 2008. ,
Prediction of signal peptides and signal anchors by a hidden Markov model, Proceedings/International Conference on Intelligent Systems for Molecular Biology, pp.122-130, 1998. ,
Improved Prediction of Signal Peptides: SignalP 3.0, Journal of Molecular Biology, vol.340, issue.4, pp.783-795, 2004. ,
DOI : 10.1016/j.jmb.2004.05.028
Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites, Protein Engineering Design and Selection, vol.10, issue.1, pp.1-6, 1997. ,
DOI : 10.1093/protein/10.1.1
A Combined Transmembrane Topology and Signal Peptide Prediction Method, Journal of Molecular Biology, vol.338, issue.5, pp.1027-1036, 2004. ,
DOI : 10.1016/j.jmb.2004.03.016
Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server, Nucleic Acids Research, vol.35, issue.Web Server, pp.429-432, 2007. ,
DOI : 10.1093/nar/gkm256
Signal peptide prediction based on analysis of experimentally verified cleavage sites, Protein Science, vol.19, issue.10, pp.2819-2824, 2004. ,
DOI : 10.1110/ps.04682504
A common export pathway for proteins binding complex redox cofactors? Molecular microbiology, pp.393-404, 1996. ,
Adaptation of protein secretion to extremely high-salt conditions by extensive use of the twinarginine translocation pathway. Molecular microbiology, pp.943-950, 2002. ,
Prediction of twinarginine signal peptides, BMC Bioinformatics, vol.6, issue.1, p.167, 2005. ,
DOI : 10.1186/1471-2105-6-167
The structure of signal peptides from bacterial lipoproteins, "Protein Engineering, Design and Selection", vol.2, issue.7, pp.531-534, 1989. ,
DOI : 10.1093/protein/2.7.531
Roles of histidine-103 and tyrosine-235 in the function of the prolipoprotein diacylglyceryl transferase of Escherichia coli., Journal of Bacteriology, vol.179, issue.9, pp.2944-2948, 1997. ,
DOI : 10.1128/jb.179.9.2944-2948.1997
Analysing the outer membrane subproteome of Methylococcus capsulatus (Bath) using proteomics and novel biocomputing tools, Archives of Microbiology, vol.11, issue.10, pp.362-377, 2006. ,
DOI : 10.1007/s00203-005-0055-7
A Database of Bacterial Lipoproteins (DOLOP) with Functional Assignments to Predicted Lipoproteins, Journal of Bacteriology, vol.188, issue.8, pp.1882761-2773, 2006. ,
DOI : 10.1128/JB.188.8.2761-2773.2006
Prediction of Lipoprotein Signal Peptides in Gram-Positive Bacteria with a Hidden Markov Model, Journal of Proteome Research, vol.7, issue.12, pp.5082-5093, 2008. ,
DOI : 10.1021/pr800162c
Prediction of lipoprotein signal peptides in Gram-negative bacteria, Protein Science, vol.53, issue.8, pp.1652-1662, 2003. ,
DOI : 10.1110/ps.0303703
The detection and classification of membrane-spanning proteins, Biochimica et Biophysica Acta (BBA) - Biomembranes, vol.815, issue.3, pp.468-476, 1985. ,
DOI : 10.1016/0005-2736(85)90375-X
TopPred II: an improved software for membrane protein structure predictions, Bioinformatics, vol.10, issue.6, pp.685-686, 1994. ,
DOI : 10.1093/bioinformatics/10.6.685
SOSUI: classification and secondary structure prediction system for membrane proteins, Bioinformatics, vol.14, issue.4, pp.378-379, 1998. ,
DOI : 10.1093/bioinformatics/14.4.378
Energetics, stability, and prediction of transmembrane helices11Edited by G. von Heijne, Journal of Molecular Biology, vol.312, issue.5, pp.927-934, 2001. ,
DOI : 10.1006/jmbi.2001.5008
TMpro web server and web service: transmembrane helix prediction through amino acid property analysis, Bioinformatics, vol.23, issue.20, pp.2795-2796, 2007. ,
DOI : 10.1093/bioinformatics/btm398
TM Finder: A prediction program for transmembrane protein segments using a combination of hydrophobicity and nonpolar phase helicity scales, Protein Science, vol.10, issue.1, pp.212-219, 2001. ,
DOI : 10.1110/ps.30301
A Model Recognition Approach to the Prediction of All-Helical Membrane Protein Structure and Topology, Biochemistry, vol.33, issue.10, pp.3038-3049, 1994. ,
DOI : 10.1021/bi00176a037
Prediction of membrane protein topology utilizing multiple sequence alignments, Journal of Protein Chemistry, vol.16, issue.5, pp.453-457, 1997. ,
DOI : 10.1023/A:1026353225758
Topology prediction for helical transmembrane proteins at 86% accuracy-Topology prediction at 86% accuracy, Protein Science, vol.227, issue.8, pp.1704-1718, 1996. ,
DOI : 10.1002/pro.5560050824
???TransMem???: a neural network implemented in Excel spreadsheets for predicting transmembrane domains of proteins, Bioinformatics, vol.13, issue.3, pp.231-234, 1997. ,
DOI : 10.1093/bioinformatics/13.3.231
Predicting transmembrane protein topology with a hidden markov model: application to complete genomes11Edited by F. Cohen, Journal of Molecular Biology, vol.305, issue.3, pp.567-580, 2001. ,
DOI : 10.1006/jmbi.2000.4315
The HMMTOP transmembrane topology prediction server, Bioinformatics, vol.17, issue.9, pp.849-850, 2001. ,
DOI : 10.1093/bioinformatics/17.9.849
Best ??-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information, Protein Science, vol.12, issue.7, pp.1908-1917, 2004. ,
DOI : 10.1110/ps.04625404
SVMtm: Support vector machines to predict transmembrane segments, Journal of Computational Chemistry, vol.312, issue.5, pp.632-636, 2004. ,
DOI : 10.1002/jcc.10411
TMB-Hunt: an amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins, BMC Bioinformatics, vol.6, issue.1, p.56, 2005. ,
DOI : 10.1186/1471-2105-6-56
A consensus algorithm to screen genomes for novel families of transmembrane ?? barrel proteins, Proteins: Structure, Function, and Bioinformatics, vol.53, issue.Suppl 6, pp.8-18, 2007. ,
DOI : 10.1002/prot.21439
Evaluation of methods for predicting the topology of beta-barrel outer membrane proteins and a consensus prediction method, BMC Bioinformatics, vol.6, issue.1, p.7, 2005. ,
DOI : 10.1186/1471-2105-6-7
A sequence-profile-based HMM for predicting and discriminating ?? barrel membrane proteins, Bioinformatics, vol.18, issue.Suppl 1, pp.46-53, 2002. ,
DOI : 10.1093/bioinformatics/18.suppl_1.S46
Predicting transmembrane beta-barrels in proteomes. Nucleic acids research, pp.2566-2577, 2004. ,
TMBpro: secondary structure, ??-contact and tertiary structure prediction of transmembrane ??-barrel proteins, Bioinformatics, vol.24, issue.4, pp.513-520, 2008. ,
DOI : 10.1093/bioinformatics/btm548
PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins, 34 Web Server, pp.186-188, 2006. ,
DOI : 10.1093/nar/gkl262
A method for discovering transmembrane beta-barrel proteins in Gram-negative bacterial proteomes, Computational Biology and Chemistry, vol.32, issue.4, pp.298-301, 2008. ,
DOI : 10.1016/j.compbiolchem.2008.03.010
transFold: a web server for predicting the structure and residue contacts of transmembrane beta-barrels, 34 Web Server, pp.189-193, 2006. ,
DOI : 10.1093/nar/gkl205
The ??-barrel finder (BBF) program, allowing identification of outer membrane ??-barrel proteins encoded within prokaryotic genomes, Protein Science, vol.4, issue.9, pp.2196-2207, 2002. ,
DOI : 10.1110/ps.0209002
BOMP: a program to predict integral ??-barrel outer membrane proteins encoded within genomes of Gram-negative bacteria, 32 Web Server, pp.394-399, 2004. ,
DOI : 10.1093/nar/gkh351
PRED-TMBB: a web server for predicting the topology of ??-barrel outer membrane proteins, 32 Web Server, pp.400-404, 2004. ,
DOI : 10.1093/nar/gkh417
Discrimination of outer membrane proteins using support vector machines, Bioinformatics, vol.21, issue.23, pp.4223-4229, 2005. ,
DOI : 10.1093/bioinformatics/bti697
TMBETADISC-RBF: Discrimination of -barrel membrane proteins using RBF networks and PSSM profiles, Computational Biology and Chemistry, vol.32, issue.3, pp.227-231, 2008. ,
DOI : 10.1016/j.compbiolchem.2008.03.002
Augur--a computational pipeline for whole genome microbial surface protein prediction and classification, Bioinformatics, vol.22, issue.22, pp.2819-2820, 2006. ,
DOI : 10.1093/bioinformatics/btl466
LocateP: Genome-scale subcellular-location predictor for bacterial proteins, BMC Bioinformatics, vol.9, issue.1, p.173, 2008. ,
DOI : 10.1186/1471-2105-9-173
Ranganathan S: SPdb?a signal peptide database, BMC Bioinformatics, vol.6, issue.1, p.249, 2005. ,
DOI : 10.1186/1471-2105-6-249
PSORTdb: a protein subcellular localization database for bacteria, 33 Database, pp.164-168, 2005. ,
DOI : 10.1093/nar/gki027
Construction of Functional Interaction Networks through Consensus Localization Predictions of the Human Proteome, Journal of Proteome Research, vol.8, issue.7, pp.3367-3376, 2009. ,
DOI : 10.1021/pr900018z
Validating subcellular localization prediction tools with mycobacterial proteins, BMC Bioinformatics, vol.10, issue.1, p.134, 2009. ,
DOI : 10.1186/1471-2105-10-134
'Unite and conquer': enhanced prediction of protein subcellular localization by integrating multiple specialized tools, BMC Bioinformatics, vol.8, issue.1, p.420, 2007. ,
DOI : 10.1186/1471-2105-8-420
The natural evolutionary relationships among prokaryotes. Critical reviews in microbiology, pp.111-131, 2000. ,
: Evidence for a novel outer membrane and for intracellular vesicle budding in an archaeon, Archaea, vol.181, issue.1, pp.9-18, 2002. ,
DOI : 10.1155/2002/307480
EcoGene: a genome sequence database for Escherichia coli K-12, Nucleic Acids Research, vol.28, issue.1, pp.60-64, 2000. ,
DOI : 10.1093/nar/28.1.60
K-12 estimated from a comparison of the genome sequences between two different substrains, FEBS Letters, vol.397, issue.1-2, pp.72-76, 1999. ,
DOI : 10.1016/S0014-5793(99)00481-0
The Complete Genome Sequence of Escherichia coli DH10B: Insights into the Biology of a Laboratory Workhorse, Journal of Bacteriology, vol.190, issue.7, pp.1902597-2606, 2008. ,
DOI : 10.1128/JB.01695-07
Characterization of the Vibrio cholerae ToxR regulon: identification of novel genes involved in intestinal colonization, Infection and immunity, issue.11, pp.562822-2829, 1988. ,
Effects of lipoprotein overproduction on the induction of DegP (HtrA) involved in quality control in the Escherichia coli periplasm. The Journal of biological chemistry, pp.27939807-39813, 2004. ,
OxyGene: an innovative platform for investigating oxidative-response genes in whole prokaryotic genomes, BMC Genomics, vol.9, issue.1, p.637, 2008. ,
DOI : 10.1186/1471-2164-9-637
URL : https://hal.archives-ouvertes.fr/hal-00357551
SecA2 functions in the secretion of superoxide dismutase A and in the virulence of Mycobacterium tuberculosis. Molecular microbiology, pp.453-464, 2003. ,
Topogenesis of membrane proteins: determinants and dynamics, FEBS Letters, vol.12, issue.3, pp.87-93, 2001. ,
DOI : 10.1016/S0014-5793(01)02712-0
Signal sequences: more than just greasy peptides, Trends in Cell Biology, vol.8, issue.10, pp.410-415, 1998. ,
DOI : 10.1016/S0962-8924(98)01360-9
Type VI secretion: a beginner's guide. Current opinion in microbiology, pp.3-8, 2008. ,
A mRNA Signal for the Type III Secretion of Yop Proteins by Yersinia enterocolitica, Science, vol.278, issue.5340, pp.2781140-1143, 1997. ,
DOI : 10.1126/science.278.5340.1140
Yersinia enterocolitica type III secretion: an mRNA signal that couples translation and secretion of YopQ, Molecular Microbiology, vol.165, issue.4, pp.1139-1148, 1999. ,
DOI : 10.1016/0378-1119(87)90365-9
Secretion of Yop proteins by Yersiniae, Infection and immunity, vol.58, issue.9, pp.2840-2849, 1990. ,
Prediction of Type III Secretion Signals in Genomes of Gram-Negative Bacteria, PLoS ONE, vol.4, issue.6, p.5917, 2009. ,
DOI : 10.1371/journal.pone.0005917.s008
Sequence-Based Prediction of Type III Secreted Proteins, PLoS Pathogens, vol.13, issue.5, p.1000376, 2009. ,
DOI : 10.1371/journal.ppat.1000376.s015
PrediSi: prediction of signal peptides and their cleavage positions, 32 Web Server, pp.375-379, 2004. ,
DOI : 10.1093/nar/gkh378
High performance system for signal peptide prediction: SOSUIsignal, Chem-Bio Informatics Journal, vol.4, issue.4, pp.142-147, 2004. ,
DOI : 10.1273/cbij.4.142
Amphiphilicity index of polar amino acids as an aid in the characterization of amino acid preference at membrane-water interfaces, Bioinformatics, vol.18, issue.4, pp.608-616, 2002. ,
DOI : 10.1093/bioinformatics/18.4.608
Basic Charge Clusters and Predictions of Membrane Protein Topology, Journal of Chemical Information and Computer Sciences, vol.42, issue.3, pp.620-632, 2002. ,
DOI : 10.1021/ci010263s
Finding beta-barrel outer membrane proteins with a Markov Chain Model, WSEAS Transactions on Biology and Biomedecine, vol.1, issue.2, pp.186-189, 2004. ,
TMBETA-NET: discrimination and prediction of membrane spanning ??-strands in outer membrane proteins, Nucleic Acids Research, vol.33, issue.Web Server, pp.164-167, 2005. ,
DOI : 10.1093/nar/gki367
TMB-Hunt: a web server to screen sequence sets for transmembrane ??-barrel proteins, Nucleic Acids Research, vol.33, issue.Web Server, pp.188-192, 2005. ,
DOI : 10.1093/nar/gki384
Predicting subcellular localization of proteins using machine-learned classifiers, Bioinformatics, vol.20, issue.4, pp.547-556, 2004. ,
DOI : 10.1093/bioinformatics/btg447
A novel representation of protein sequences for prediction of subcellular location using support vector machines, Protein Science, vol.451, issue.11, pp.2804-2813, 2005. ,
DOI : 10.1110/ps.051597405
URL : https://hal.archives-ouvertes.fr/hal-00433582
Support vector machine approach for protein subcellular localization prediction, Bioinformatics, vol.17, issue.8, pp.721-728, 2001. ,
DOI : 10.1093/bioinformatics/17.8.721
Using AdaBoost for the prediction of subcellular location of prokaryotic and eukaryotic proteins, Molecular Diversity, vol.17, issue.5, pp.41-45, 2008. ,
DOI : 10.1007/s11030-008-9073-0
SOSUI-GramN: high performance prediction for sub-cellular localization of proteins in Gram-negative bacteria, Bioinformation, vol.2, issue.9, pp.417-421, 2008. ,
DOI : 10.6026/97320630002417
EchoLOCATION: an in silico analysis of the subcellular locations of Escherichia coli proteins and comparison with experimentally derived locations, Bioinformatics, vol.25, issue.2, pp.163-166, 2009. ,
DOI : 10.1093/bioinformatics/btn596
THGS: a web-based database of Transmembrane Helices in Genome Sequences, Nucleic Acids Research, vol.32, issue.90001, pp.32-125, 2004. ,
DOI : 10.1093/nar/gkh130
PREDICTION OF CELL WALL SORTING SIGNALS IN GRAM-POSITIVE BACTERIA WITH A HIDDEN MARKOV MODEL: APPLICATION TO COMPLETE GENOMES, Journal of Bioinformatics and Computational Biology, vol.06, issue.02, pp.387-401, 2008. ,
DOI : 10.1142/S0219720008003382
HHomp--prediction and classification of outer membrane proteins, 37 Web Server, pp.446-451, 2009. ,
DOI : 10.1093/nar/gkp325
Identification of putative exported/secreted proteins in prokaryotic proteomes, Gene, vol.269, issue.1-2, pp.195-204, 2001. ,
DOI : 10.1016/S0378-1119(01)00436-X
Prediction of signal peptides in archaea, Protein Engineering Design and Selection, vol.22, issue.1, pp.27-35, 2009. ,
DOI : 10.1093/protein/gzn064
TMPDB: a database of experimentally-characterized transmembrane topologies, Nucleic Acids Research, vol.31, issue.1, pp.406-409, 2003. ,
DOI : 10.1093/nar/gkg020
TOPDB: topology data bank of transmembrane proteins, 36 Database, pp.234-239, 2008. ,
DOI : 10.1093/nar/gkm751
A comparison of signal sequence prediction methods using a test set of signal peptides, Bioinformatics, vol.16, issue.8, pp.741-742, 2000. ,
DOI : 10.1093/bioinformatics/16.8.741
LIPPRED: A web server for accurate prediction of lipoprotein signal sequences and cleavage sites, Bioinformation, vol.1, issue.5, pp.176-179, 2006. ,
DOI : 10.6026/97320630001176
SPEPlip: the detection of signal peptide and lipoprotein cleavage sites, Bioinformatics, vol.19, issue.18, pp.2498-2499, 2003. ,
DOI : 10.1093/bioinformatics/btg360
Non-classical protein secretion in bacteria, BMC Microbiology, vol.5, issue.1, p.58, 2005. ,
DOI : 10.1186/1471-2180-5-58
Signal-3L: A 3-layer approach for predicting signal peptides, Biochemical and Biophysical Research Communications, vol.363, issue.2, pp.297-303, 2007. ,
DOI : 10.1016/j.bbrc.2007.08.140
Signal-CF: A subsite-coupled and window-fusing approach for predicting signal peptides, Biochemical and Biophysical Research Communications, vol.357, issue.3, pp.633-640, 2007. ,
DOI : 10.1016/j.bbrc.2007.03.162
High-performance signal peptide prediction based on sequence alignment techniques, Bioinformatics, vol.24, issue.19, pp.2172-2176, 2008. ,
DOI : 10.1093/bioinformatics/btn422
Identification of Diverse Archaeal Proteins with Class III Signal Peptides Cleaved by Distinct Archaeal Prepilin Peptidases, Journal of Bacteriology, vol.189, issue.3, pp.772-778, 2007. ,
DOI : 10.1128/JB.01547-06
Domain Organization of Long Signal Peptides of Single-Pass Integral Membrane Proteins Reveals Multiple Functional Capacity, PLoS ONE, vol.102, issue.7, p.2767, 2008. ,
DOI : 10.1371/journal.pone.0002767.s003
Transmembrane Topology and Signal Peptide Prediction Using Dynamic Bayesian Networks, PLoS Computational Biology, vol.18, issue.11, p.1000213, 2008. ,
DOI : 10.1371/journal.pcbi.1000213.t008
OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar, Bioinformatics, vol.24, issue.15, pp.1662-1668, 2008. ,
DOI : 10.1093/bioinformatics/btn221
SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology, Bioinformatics, vol.24, issue.24, pp.2928-2929, 2008. ,
DOI : 10.1093/bioinformatics/btn550
MemBrain: Improving the Accuracy of Predicting Transmembrane Helices, PLoS ONE, vol.301, issue.6, p.2399, 2008. ,
DOI : 10.1371/journal.pone.0002399.s004
Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: the dense alignment surface method, Protein Engineering Design and Selection, vol.10, issue.6, pp.673-676, 1997. ,
DOI : 10.1093/protein/10.6.673
Algorithms for incorporating prior topological information in HMMs: application to transmembrane proteins, BMC Bioinformatics, vol.7, issue.1, p.189, 2006. ,
DOI : 10.1186/1471-2105-7-189
Enhanced Membrane Protein Topology Prediction Using a Hierarchical Classification Method and a New Scoring Function, Journal of Proteome Research, vol.7, issue.2, pp.487-496, 2008. ,
DOI : 10.1021/pr0702058
Predicting the topology of transmembrane helical proteins using mean burial propensity and a hidden-Markov-model-based method, Protein Science, vol.49, issue.7, pp.1547-1555, 2003. ,
DOI : 10.1110/ps.0305103
waveTM: waveletbased transmembrane segment prediction, Silico Biol, vol.4, issue.2, pp.127-131, 2004. ,
A novel method for predicting transmembrane segments in proteins based on a statistical analysis of the SwissProt database: the PRED-TMR algorithm, Protein Engineering Design and Selection, vol.12, issue.5, pp.381-385, 1999. ,
DOI : 10.1093/protein/12.5.381
URL : https://hal.archives-ouvertes.fr/hal-00170724
IgTM: An algorithm to predict transmembrane domains and topology in proteins, BMC Bioinformatics, vol.9, issue.1, p.367, 2008. ,
DOI : 10.1186/1471-2105-9-367
TOPCONS: consensus prediction of membrane protein topology, 37 Web Server, pp.465-468, 2009. ,
DOI : 10.1093/nar/gkp363
Web-based toolkits for topology prediction of transmembrane helical proteins, fold recognition, structure and binding scoring, folding-kinetics analysis and comparative analysis of domain combinations, Nucleic Acids Research, vol.33, issue.Web Server, pp.193-197, 2005. ,
DOI : 10.1093/nar/gki360
ConPred II: a consensus prediction method for obtaining transmembrane topology models with high reliability, 32 Web Server, pp.390-393, 2004. ,
DOI : 10.1093/nar/gkh380
Improving the accuracy of transmembrane protein topology prediction using evolutionary information, Bioinformatics, vol.23, issue.5, pp.538-544, 2007. ,
DOI : 10.1093/bioinformatics/btl677
Combining prediction of secondary structure and solvent accessibility in proteins, Proteins: Structure, Function, and Bioinformatics, vol.10, issue.3, pp.467-475, 2005. ,
DOI : 10.1002/prot.20441
Transmembrane helix prediction using amino acid property features and latent semantic analysis, BMC Bioinformatics, vol.9, issue.Suppl 1, p.4, 2008. ,
DOI : 10.1186/1471-2105-9-S1-S4
Protein secondary structure prediction based on position-specific scoring matrices, Journal of Molecular Biology, vol.292, issue.2, pp.195-202, 1999. ,
DOI : 10.1006/jmbi.1999.3091
Protein structure prediction servers at University College London, Nucleic Acids Research, vol.33, issue.Web Server, pp.36-38, 2005. ,
DOI : 10.1093/nar/gki410
URL : http://doi.org/10.1093/nar/gki410
NPS@: Network Protein Sequence Analysis, Trends in Biochemical Sciences, vol.25, issue.3, pp.147-150, 2000. ,
DOI : 10.1016/S0968-0004(99)01540-6
URL : https://hal.archives-ouvertes.fr/hal-00313012
HMM-based protein structure prediction, 37 Web Server, pp.492-497, 2009. ,
Porter: a new, accurate server for protein secondary structure prediction, Bioinformatics, vol.21, issue.8, pp.1719-1720, 2005. ,
DOI : 10.1093/bioinformatics/bti203
An improved hidden Markov model for transmembrane protein detection and topology prediction and its applications to complete genomes, Bioinformatics, vol.21, issue.9, pp.1853-1858, 2005. ,
DOI : 10.1093/bioinformatics/bti303
A simple and fast secondary structure prediction method using hidden neural networks, Bioinformatics, vol.21, issue.2, pp.152-159, 2005. ,
DOI : 10.1093/bioinformatics/bth487
MemType-2L: A Web server for predicting membrane proteins and their types by incorporating evolution information through Pse-PSSM, Biochemical and Biophysical Research Communications, vol.360, issue.2, pp.339-345, 2007. ,
DOI : 10.1016/j.bbrc.2007.06.027
Prediction of protein subcellular localization, Proteins: Structure, Function, and Bioinformatics, vol.63, issue.3, pp.643-651, 2006. ,
DOI : 10.1002/prot.21018
Protein subcellular localization prediction based on compartment-specific features and structure conservation, BMC Bioinformatics, vol.8, issue.1, p.330, 2007. ,
DOI : 10.1186/1471-2105-8-330
PSLpred: prediction of subcellular localization of bacterial proteins, Bioinformatics, vol.21, issue.10, pp.2522-2524, 2005. ,
DOI : 10.1093/bioinformatics/bti309
Large-Scale Predictions of Gram-Negative Bacterial Protein Subcellular Locations, Journal of Proteome Research, vol.5, issue.12, pp.3420-3428, 2006. ,
DOI : 10.1021/pr060404b
Gpos-PLoc: an ensemble classifier for predicting subcellular localization of Gram-positive bacterial proteins, Protein Engineering Design and Selection, vol.20, issue.1, pp.39-46, 2007. ,
DOI : 10.1093/protein/gzl053
Mimicking Cellular Sorting Improves Prediction of Subcellular Localization, Journal of Molecular Biology, vol.348, issue.1, pp.85-100, 2005. ,
DOI : 10.1016/j.jmb.2005.02.025
Prediction of subcellular protein localization based on functional domain composition, Biochemical and Biophysical Research Communications, vol.357, issue.2, pp.366-370, 2007. ,
DOI : 10.1016/j.bbrc.2007.03.139
Support Vector Machine-based method for predicting subcellular localization of mycobacterial proteins using evolutionary information and motifs, BMC Bioinformatics, vol.8, issue.1, p.337, 2007. ,
DOI : 10.1186/1471-2105-8-337
Lipoprotein computational prediction in spirochaetal genomes, Microbiology, vol.152, issue.1, pp.113-121, 2006. ,
DOI : 10.1099/mic.0.28317-0
PROTEUS2: a web server for comprehensive protein structure prediction and structure-based annotation, 36 Web Server, pp.202-209, 2008. ,
DOI : 10.1093/nar/gkn255
An hierarchical artificial neural network system for the classification of transmembrane proteins, Protein Engineering Design and Selection, vol.12, issue.8, pp.631-634, 1999. ,
DOI : 10.1093/protein/12.8.631
URL : https://hal.archives-ouvertes.fr/hal-00170718
BPROMPT: a consensus server for membrane protein prediction, Nucleic Acids Research, vol.31, issue.13, pp.313698-3700, 2003. ,
DOI : 10.1093/nar/gkg554
A novel tool for the prediction of transmembrane protein topology based on a statistical analysis of the SwissProt database: the OrienTM algorithm, Protein Engineering Design and Selection, vol.14, issue.6, pp.387-390, 2001. ,
DOI : 10.1093/protein/14.6.387
URL : https://hal.archives-ouvertes.fr/hal-01154852
APSSP2: A combination method for protein secondary structure prediction based on neural network and example based learning, p.132, 2002. ,
PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information, Nucleic Acids Research, vol.33, issue.Web Server, pp.289-294, 2005. ,
DOI : 10.1093/nar/gki390
OPM: Orientations of Proteins in Membranes database, Bioinformatics, vol.22, issue.5, pp.623-625, 2006. ,
DOI : 10.1093/bioinformatics/btk023
MPtopo: A database of membrane protein topology, Protein Science, vol.10, issue.2, pp.455-458, 2001. ,
DOI : 10.1110/ps.43501
PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank, 33 Database, pp.275-278, 2005. ,
DOI : 10.1093/nar/gki002
TMBETA-GENOME: database for annotated ??-barrel membrane proteins in genomic sequences, Database, pp.35-314, 2007. ,
DOI : 10.1093/nar/gkl805
The PredictProtein server, 32 Web Server, pp.321-326, 2004. ,
EcoProDB: the Escherichia coli protein database, Bioinformatics, vol.23, issue.18, pp.2501-2503, 2007. ,
DOI : 10.1093/bioinformatics/btm351
LOCnet and LOCtarget: sub-cellular localization for structural genomics targets, 32 Web Server, pp.517-521, 2004. ,
DOI : 10.1093/nar/gkh441
DBMLoc: a Database of proteins with multiple subcellular localizations, BMC Bioinformatics, vol.9, issue.1, p.127, 2008. ,
DOI : 10.1186/1471-2105-9-127
CoBaltDB: Complete bacterial and archaeal orfeomes subcellular localization database and associated resources, BMC Microbiology, vol.10, issue.1, p.88, 2010. ,
DOI : 10.1186/1471-2180-10-88