title: MemPype: a pipeline for the annotation of eukaryotic membrane proteins.
abstract: MemPype is a Python-based pipeline including previously published methods for the prediction of signal peptides (SPEP), glycophosphatidylinositol (GPI) anchors (PredGPI), all-alpha membrane topology (ENSEMBLE), and a recent method (MemLoci) that specifically discriminates the localization of eukaryotic membrane proteins in: 'cell membrane', 'internal membranes', 'organelle membranes'. MemLoci scores with accuracy of 70% and generalized correlation coefficient (GCC) of 0.50 on a rigorous homology-unbiased validation set and overpasses other predictors for subcellular localization. The annotation process is based both on inheritance through homology and computational methods. Each submitted protein first retrieves, when available, up to 25 similar proteins (with sequence identity ≥50% and alignment coverage ≥50% on both sequences). This helps the identification of membrane-associated proteins and detailed localization tags. Each protein is also filtered for the presence of a GPI anchor [0.8% false positive rate (FPR)]. A positive score of GPI anchor prediction labels the sequence as exposed to 'Cell surface'. Concomitantly the sequence is analysed for the presence of a signal peptide and classified with MemLoci into one of three discriminated classes. Finally the sequence is filtered for predicting its putative all-alpha protein membrane topology (FPR <1%). The web server is available at: http://mu2py.biocomp.unibo.it/mempype.
authors.affiliation: Externautics s.p.a.-Bioinformatics, Via Fiorentina 1, 53100 Siena, Italy. andrea.pierleoni@externautics.com
authors.forename: Andrea
authors.initials: A
authors.lastname: Pierleoni
authors.forename: Valentina
authors.initials: V
authors.lastname: Indio
authors.forename: Castrense
authors.initials: C
authors.lastname: Savojardo
authors.forename: Piero
authors.initials: P
authors.lastname: Fariselli
authors.forename: Pier Luigi
authors.initials: PL
authors.lastname: Martelli
authors.forename: Rita
authors.initials: R
authors.lastname: Casadio
mesh_terms: D058851:GPI-Linked Proteins / Q000737:chemistry; D008565:Membrane Proteins / Q000032:analysis / Q000737:chemistry*; D058977:Molecular Sequence Annotation; D021382:Protein Sorting Signals; D017434:Protein Structure, Tertiary; D017386:Sequence Homology, Amino Acid; D012984:Software
chemical_list: D058851:GPI-Linked Proteins; D008565:Membrane Proteins; D021382:Protein Sorting Signals