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Examples of proteome predictions for three organism typesEukaryota - Human proteom GRCh37.62
Gram positive bacteria - B.subtilis EB2
Gram negative bacteria - E.coli K12
Training and testing data setsThese are the annotated sequence data described in Table A of the Supplementary Materials. The entire datasets correspond to the "Total" columns in the table (before homology reduction). Sequences labeled "Train" correspond to the "Train" columns in the table, while sequences labeled "Evaluation" correspond to the "Comp." columns in the table (used for comparing the performance to SignalP 3.0 and other methods). Sequences used to train SignalP 3.0 (or homologous to those used to train SignalP 3.0) have been removed from the "Comp." sets.Note that the "Comp." sets are subsets of the "Train" sets. The evaluation of SignalP 4.0 was done using a nested cross-validation approach, where different partitions were used for training, optimization and evaluation, see Supplementary Materials for details. 166 AJL2_ANGJA Evaluation MVSFKLPAFLCVAVLSSMALVSHGAVLGLCEGACPEGWVEHKNRCYLHVAEKKTWLDAELNCLHHGGNLASEHSEDEHQF LKDLHKGSDDPFWIGLSAVHEGRSWLWSDGTSASAEGDFSMWNPGEPNDAGGKEDCVHDNYGGQKHWNDIKCDLLFPSIC VLRMVE SSSSSSSSSSSSSSSSSSSSSSSS........................................................ ................................................................................ ...... 503 A1BG_BOVIN Evaluation Train MSAWAALLLLWGLSLSPVTEQATFFDPRPSLWAEAGSPLAPWADVTLTCQSPLPTQEFQLLKDGVGQEPVHLESPAHEHR FPLGPVTSTTRGLYRCSYKGNNDWISPSNLVEVTGAEPLPAPSISTSPVSWITPGLNTTLLCLSGLRGVTFLLRLEGEDQ FLEVAEAPEATQATFPVHRAGNYSCSYRTHAAGTPSEPSATVTIEELDPPPAPTLTVDRESAKVLRPGSSASLTCVAPLS GVDFQLRRGAEEQLVPRASTSPDRVFFRLSALAAGDGSGYTCRYRLRSELAAWSRDSAPAELVLSDGTLPAPELSAEPAI LSPTPGALVQLRCRAPRAGVRFALVRKDAGGRQVQRVLSPAGPEAQFELRGVSAVDSGNYSCVYVDTSPPFAGSKPSATL ELRVDGPLPRPQLRALWTGALTPGRDAVLRCEAEVPDVSFLLLRAGEEEPLAVAWSTHGPADLVLTSVGPQHAGTYSCRY RTGGPRSLLSELSDPVELRVAGS SSSSSSSSSSSSSSSSSSSSS........................................................... ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ .......................The format is:
S — Amino acid is part of a Signal peptide (experimentally verified) T — Amino acid is part of a Transmembrane region (experimentally verified) t — Amino acid is part of a Transmembrane region (not experimentally verified) . — An annotation different from those shown above
Eukaryota sequence data
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