EPipe 0.974 Server BETA version, return comments

The EPipe 0.974 server performs comparative analysis of protein sequences derived from the same transcript by alternative splicing, genome variation data (SNPs) or protein families from one or more organisms. The analysis is automated: the input proteins are first processed by a number of analysis and prediction methods, the results are then remapped onto a multiple alignment and compared. All the differences found between the variants are reported in detail. It is also possible to view the complete analysis and prediction results.

NOTE 1:   This service is under development; new analysis and prediction methods are being added, the output format is being refined etc. As many external tools are called special attention is given to the overall speed of the service. Documentation is in preparation.

NOTE 2:   EPipe is dependent on a number of other programs that have to be run on the input sequences prior to the comparative analysis. Therefore, the processing of multiple sequences may be time-consuming. In the case of prolonged wait the user is advised to use the e-mail option: at any time during the wait you may enter your e-mail address and simply leave the window. Your job will continue; you will be notified by e-mail when it has terminated. The e-mail message will contain the URL under which the results are stored; they will remain on the server for 24 hours for you to collect them.

Instructions

Output format

Article abstract

Specify the input

Input sequences	Paste a single or several amino acid sequences in FASTA format into the field below: or submit a file in FASTA format directly from your local disk:
Multiple alignment	Yes, let EPipe align the input sequences according to the settings below No, the input sequences are provided as alignment

Alignment method	MAFFT T-COFFEE CLUSTAL DIALIGN HMM align
Alignment parameters	Gap open penalty Gap extension penalty Gap open penalty Gap extension penalty End gap separation penalty OFFON Gap separation penalty range (no options required)
Gene sequence of unspliced transcript (not implemented yet)	Unspliced transcript in FASTA format (DNA)

Select features for analysis

The feature list below has been structured according the emerging classification scheme of the BioSapiens Ontology.




Non-positional (not implemented yet)  »  ontology: BS:00127

     Miscellaneous

          

		Mass	Molecular weight (kDa)
		Secretory	Secretory protein (SignalP)
		SecretomeP	Non-classical protein secretion
		WolfPSort	Protein Subcellular Localization Prediction

Positional  »  ontology: BS:00129

     Database matches

          

		Hit to PDB	Best match in PDB
		Pfam 3.0	Protein domains and families
		Superfamily	HMM database of structural and functional annotation for all proteins and genomes

     Protein Structure  »  ontology: structural_region

          

		PDB-DSSP	DSSP assignments of the best match in PDB
		IUpred	Intrinsically unstructured regions
		PSIPRED 2.5	Secondary structure predictions
		NetSurfP 1.0a	Protein Surface Accessibility and Secondary Structure Predictions
		Leucine zipper predictor	Leucine zipper predictor
		RADAR	Rapid Automatic Detection and Alignment of Repeats in protein sequences
		DisEMBL	Intrinsic Protein Disorder Prediction

     Post-translational modification  »  ontology: post_translationally_modified_region

          

		NetPhos 3.1b	Phosphorylation sites
		NetOGlyc 3.1d	O-GalNAc (mucin type) glycosylation sites
		NetNGlyc 1.0a	N-linked glycosylation sites
		YinOYang	O-glyc sites on intracellular/nuclear, often signaling, proteins
		NetCGlyc 1.0a	C-mannosylation sites in mammalian proteins
		NetAcet 1.0	Predicts substrates of N-acetyltransferase A (NatA)
		NetGlycate 1.0	Predicts glycation of e amino groups of lysines in mammalian proteins
		NetPhorest 1.0	Sequence-based classifiers for linear motifs in phosphorylation-dependent signaling
		KEPE 1.0	Sumoylation site
		USP7_2 1.0	USP7 binding motif (USP7/HAUSP, a de-ubiquitinating enzyme)
		ASX_betaOH_EGF 1.0	ASX EGF hydroxylation
		CAAXbox 1.0	CAAX Box
		CMANNOS 1.0	C-Mannosylation site (on W)
		SPalmitoyl_2 1.0	S-palmitoylation site (on C)
		SPalmitoyl_4 1.0	S-palmitoylation site (on C)
		WntLipid 1.0	Wnt-Wingless palmitoylation site

     Peptide cleavage  »  ontology: cleaved_peptide_region

          

		SignalP 4.0	Secretory signal peptides including cleavage sites
		ProP	Propeptide cleavage sites
		TASPASE1 1.0	Taspase1 cleavage site

     Membrane structure  »  ontology: membrane_structure

          

		TMHMM 2.0c	Transmembrane helices
		Phobius predictor	Phobius transmembrane topology and signal peptides predictor

     Localisation signal  »  ontology:

          

		ER_KDEL_1 1.0	KDEL retrieving signals
		ER_diLys_1 1.0	Di-lysine ER retrieving signal
		Golgi_diPhe_1 1.0	ER export signals

     Binding motif  »  ontology:

          

		AP2alpha_1 1.0	AP2 alpha ligands
		AP2alpha_2 1.0	AP2 alpha ligands
		APCC_Dbox_1 1.0	APCC-binding Destruction motifs
		APCC_KENbox_2 1.0	APCC-binding Destruction motifs
		AP_GAE_1 1.0	Gamma-adaptin ear interaction motif
		BRCT_MDC1_1 1.0	BRCT phosphopeptide ligands
		CAP-Gly_1 1.0	CAP-Gly Domain Ligand
		COP1 1.0	COP1 binding motif
		Clathr_ClatBox_2 1.0	Clathrin box
		Dynein_DLC8_1 1.0	Dynein (Light Chain) binding motifs
		EH_1 1.0	eh1 motif
		EVH1_I 1.0	EVH1 ligand
		EVH1_II 1.0	EVH1 ligand
		GYF 1.0	GYF ligand
		HOMEOBOX 1.0	Homeodomain ligand
		IBS_1 1.0	Integrin binding sites
		MAPK_2 1.0	MAPK docking motif
		RGD 1.0	Integrin binding sites
		SIAH_1 1.0	Siah binding Motif
		TNKBM 1.0	Tankyrase-binding motif
		TPR 1.0	TPR binding site
		TRAF2_2 1.0	TRAF2 binding site
		ULM_U2AF65_1 1.0	UHM domain ligand
		WH1 1.0	WH1 ligand
		WRPW_1 1.0	WRPW motif
		WRPW_2 1.0	WRPW motif

     Miscellaneous

          

		I-mutant 2.0.4
		NetNES	Nuclear export signals
		PredictNLS	NLS

Restrictions:
At most ? sequences and ? amino acids per submission; each sequence not less than ? and not more than ? amino acids.

Confidentiality:
The sequences are kept confidential and will be deleted after processing.

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CITATION

For publication of results, please cite:

Protein annotation in the era of personal genomics.
Blicher T, Gupta R, Wesolowska A, Jensen LJ, Brunak S.
Curr Opin Struct Biol., 20:335-41, 2010.

EPipe 1.0: a pipeline for discovery of functional differences in proteins originating from alternative splicing, pan-genome variation or protein family evolution.
In preparation by several groups from the BioSapiens Network of Excellence, 2008.

The pipeline also relates to the work described in:

The implications of alternative splicing in the ENCODE protein complement.
Tress, ML et al.
Proc Natl Acad Sci U S A, 104:5495-5000, 2007.