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Data sets used in the construction and evaluation of TargetP
Data sets redundancy reduced on presequence + first amino acid of mature protein if not
otherwise stated.
Plant predictor data sets
Chloroplast (cTP) sequences
number: 141 fasta AC numbers
Comments: SWISS-PROT release 36. Only plant proteins are included -- i.e. no algae.
Mitochondrial (mTP) sequences
number: 368 fasta AC numbers
Comments: SWISS-PROT release 36. Plant and non-plant proteins (*).
Secretory Pathway/Signal Peptide (SP) sequences
number: 269 fasta AC numbers
Comments: SWISS-PROT release 36.
Nuclear sequences
number: 48 fasta AC numbers (redundancy reduced on 112 N-term.
aa's)
number: 54 fasta AC numbers (redundancy reduced on 68 N-term.
aa's)
Comments: SWISS-PROT release 36. Redundancy reduced on different lengths to be used in training of
different 1st layer networks (see article).
Cytosolic sequences
number: 87 fasta AC numbers (redundancy reduced on 112 N-term.
aa's)
number: 108 fasta AC numbers (redundancy reduced on 68 N-term.
aa's)
Comments: SWISS-PROT release 36. Redundancy reduced on different lengths to be used in training of
different 1st layer networks (see article).
The set of 940 proteins used in Tables 1 and 2 in the JMB article consists of the cTP, mTP, SP,
nuclear(54), and cytosolic(108) sets. The "other" set (162 entries) is a concatenation of the nuclear and
cytosolic sets.
Non-plant predictor data sets
Mitochondrial (mTP) sequences
number: 371 fasta AC numbers (redundancy reduced on mTP+3 aa)
Comments: SWISS-PROT release 38. Plant and non-plant proteins (*).
Secretory Pathway/Signal Peptide (SP) sequences
number: 715 fasta AC numbers
Comments: SWISS-PROT release 37.
Nuclear sequences
number: 1214 fasta AC numbers (redundancy reduced on 68 N-term.
aa's)
Comments: SWISS-PROT release 37.
Cytosolic sequences
number: 438 fasta AC numbers (redundancy reduced on 68 N-term.
aa's)
Comments: SWISS-PROT release 37.
The set of 2738 proteins used in Tables 1 and 2 in the JMB article consists of the mTP, SP,
nuclear, and cytosolic sets. The "other" set (1652 entries) is a concatenation of the nuclear and
cytosolic sets.
(*) These data sets contain both plant and non-plant mTPs as justified by a study by Schneider
et al., Proteins, 30, 49-60 (1998).
SWISS-PROT (Switzerland)
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