Mercurial > repos > peterjc > tmhmm_and_signalp

annotate tools/protein_analysis/signalp3.xml @ 2:747cec3192d3

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Migrated tool version 0.0.5 from old tool shed archive to new tool shed repository
author peterjc
date Tue, 07 Jun 2011 17:38:43 -0400
parents 9a8a7f680dd6
children fe10f448d641
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
1 <tool id="signalp3" name="SignalP 3.0" version="0.0.3">
0
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
2 <description>Find signal peptides in protein sequences</description>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
3 <command interpreter="python">
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
4 signalp3.py $organism $truncate 8 $fasta_file $tabular_file
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
5 ##I want the number of threads to be a Galaxy config option...
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
6 </command>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
7 <inputs>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
8 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
9 <param name="organism" type="select" display="radio" label="Organism">
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
10 <option value="euk">Eukaryote</option>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
11 <option value="gram+">Gram positive</option>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
12 <option value="gram-">Gram negative</option>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
13 </param>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
14 <param name="truncate" type="integer" label="Truncate sequences to this many amino acids" value="60" help="Use zero for no truncation, maximum value 6000">
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
15 <validator type="in_range" min="0" max="6000" message="Truncation value should be at most 6000. Use zero for no truncation."/>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
16 </param>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
17 </inputs>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
18 <outputs>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
19 <data name="tabular_file" format="tabular" label="SignalP $organism results" />
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
20 </outputs>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
21 <requirements>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
22 <requirement type="binary">signalp</requirement>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
23 </requirements>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
24 <tests>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
25 <test>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
26 <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta"/>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
27 <param name="organism" value="euk"/>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
28 <param name="truncate" value="0"/>
1
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
29 <output name="tabular_file" file="four_human_proteins.signalp3.tabular" ftype="tabular"/>
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
30 </test>
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
31 <test>
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
32 <param name="fasta_file" value="empty.fasta" ftype="fasta"/>
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
33 <param name="organism" value="euk"/>
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
34 <param name="truncate" value="60"/>
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
35 <output name="tabular_file" file="empty_signalp3.tabular" ftype="tabular"/>
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
36 </test>
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
37 <test>
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
38 <param name="fasta_file" value="empty.fasta" ftype="fasta"/>
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
39 <param name="organism" value="gram+"/>
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
40 <param name="truncate" value="80"/>
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
41 <output name="tabular_file" file="empty_signalp3.tabular" ftype="tabular"/>
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
42 </test>
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
43 <test>
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
44 <param name="fasta_file" value="empty.fasta" ftype="fasta"/>
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
45 <param name="organism" value="gram-"/>
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
46 <param name="truncate" value="0"/>
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
47 <output name="tabular_file" file="empty_signalp3.tabular" ftype="tabular"/>
0
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
48 </test>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
49 </tests>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
50 <help>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
51
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
52 **What it does**
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
53
1
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
54 This calls the SignalP v3.0 tool for prediction of signal peptides, which uses both a Neural Network (NN) and Hidden Markov Model (HMM) to produce two sets of scores.
0
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
55
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
56 The input is a FASTA file of protein sequences, and the output is tabular with twenty columns (one row per protein):
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
57
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
58 * Sequence identifier
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
59 * Neural Network (NN) predictions (13 columns)
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
60 * Hidden Markov Model (HMM) predictions (6 columns)
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
61
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
62 Internally the input FASTA file is divided into parts (to allow multiple processors to be used), and the proteins truncated as specified (see below). The raw output from SignalP is then reformatted into a tabular layout suitable for Galaxy (see below).
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
63
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
64 **Neural Network Scores**
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
65
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
66 For each organism class (Eukaryote, Gram-negative and Gram-positive), two different neural networks are used, one for predicting the actual signal peptide and one for predicting the position of the signal peptidase I (SPase I) cleavage site.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
67
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
68 The NN output comprises three different scores (C-max, S-max and Y-max) and two scores derived from them (S-mean and D-score).
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
69
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
70 The C-score is the 'cleavage site' score. For each position in the submitted sequence, a C-score is reported, which should only be significantly high at the cleavage site. Confusion is often seen with the position numbering of the cleavage site. When a cleavage site position is referred to by a single number, the number indicates the first residue in the mature protein, meaning that a reported cleavage site between amino acid 26-27 corresponds to that the mature protein starts at (and include) position 27.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
71
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
72 The S-score for the signal peptide prediction is calculateded for every single amino acid position in the submitted sequence (not shown in the output via Galaxy), with high scores indicating that the corresponding amino acid is part of a signal peptide, and low scores indicating that the amino acid is part of a mature protein.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
73
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
74 Y-max is a derivative of the C-score combined with the S-score resulting in a better cleavage site prediction than the raw C-score alone. This is due to the fact that multiple high-peaking C-scores can be found in one sequence, where only one is the true cleavage site. The cleavage site is assigned from the Y-score where the slope of the S-score is steep and a significant C-score is found.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
75
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
76 The S-mean is the average of the S-score, ranging from the N-terminal amino acid to the amino acid assigned with the highest Y-max score, thus the S-mean score is calculated for the length of the predicted signal peptide. The S-mean score was in SignalP version 2.0 used as the criteria for discrimination of secretory and non-secretory proteins.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
77
1
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
78 The D-score was introduced in SignalP version 3.0 and is a simple average of the S-mean and Y-max score. The score shows superior discrimination performance of secretory and non-secretory proteins to that of the S-mean score which was used in SignalP version 1 and 2.
0
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
79
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
80 For non-secretory proteins all the scores represented in the SignalP3-NN output should ideally be very low.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
81
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
82 **Hidden Markov Model Scores**
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
83
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
84 The hidden Markov model calculates the probability of whether the submitted sequence contains a signal peptide or not. The eukaryotic HMM model also reports the probability of a signal anchor, previously named uncleaved signal peptides. Furthermore, the cleavage site is assigned by a probability score together with scores for the n-region, h-region, and c-region of the signal peptide, if such one is found.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
85
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
86 The 'type' column uses 'S' for a signal peptide (i.e. secretory protein) and 'Q' for non-secretory protein.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
87
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
88 **Notes**
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
89
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
90 The raw output 'short' output from TMHMM v2.0 looks something like this (21 columns space separated - shown here formatted nicely). Notice that the identifiers are given twice, the first time truncated (as part of the NN predictions) and the second time in full (in the HMM predictions).
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
91
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
92 ==================== ===== === = ===== === = ===== === = ===== = ===== = =================================== = ===== === = ===== =
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
93 # SignalP-NN euk predictions # SignalP-HMM euk predictions
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
94 ----------------------------------------------------------------------------- ------------------------------------------------------------
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
95 # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? D ? # name ! Cmax pos ? Sprob ?
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
96 gi|2781234|pdb|1JLY| 0.061 17 N 0.043 17 N 0.199 1 N 0.067 N 0.055 N gi|2781234|pdb|1JLY|B Q 0.000 17 N 0.000 N
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
97 gi|4959044|gb|AAD342 0.099 191 N 0.012 38 N 0.023 12 N 0.014 N 0.013 N gi|4959044|gb|AAD34209.1|AF069992_1 Q 0.000 0 N 0.000 N
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
98 gi|671626|emb|CAA856 0.139 381 N 0.020 8 N 0.121 4 N 0.067 N 0.044 N gi|671626|emb|CAA85685.1| Q 0.000 0 N 0.000 N
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
99 gi|3298468|dbj|BAA31 0.208 24 N 0.184 38 N 0.980 32 Y 0.613 Y 0.398 N gi|3298468|dbj|BAA31520.1| Q 0.066 24 N 0.139 N
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
100 ==================== ===== === = ===== === = ===== === = ===== = ===== = =================================== = ===== === = ===== =
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
101
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
102 In order to make this easier to use in Galaxy, the wrapper script simplifies this to remove the redundant column and use tabs for separation. It also includes a header line with unique column names.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
103
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
104 =================================== ============= =========== ============ ============= =========== ============ ============= =========== ============ ============== ============= ========== ========= ======== ============== ============ ============= =============== ==============
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
105 #ID NN_Cmax_score NN_Cmax_pos NN_Cmax_pred NN_Ymax_score NN_Ymax_pos NN_Ymax_pred NN_Smax_score NN_Smax_pos NN_Smax_pred NN_Smean_score NN_Smean_pred NN_D_score NN_D_pred HMM_type HMM_Cmax_score HMM_Cmax_pos HMM_Cmax_pred HMM_Sprob_score HMM_Sprob_pred
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
106 gi|2781234|pdb|1JLY|B 0.061 17 N 0.043 17 N 0.199 1 N 0.067 N 0.055 N Q 0.000 17 N 0.000 N
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
107 gi|4959044|gb|AAD34209.1|AF069992_1 0.099 191 N 0.012 38 N 0.023 12 N 0.014 N 0.013 N Q 0.000 0 N 0.000 N
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
108 gi|671626|emb|CAA85685.1| 0.139 381 N 0.020 8 N 0.121 4 N 0.067 N 0.044 N Q 0.000 0 N 0.000 N
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
109 gi|3298468|dbj|BAA31520.1| 0.208 24 N 0.184 38 N 0.980 32 Y 0.613 Y 0.398 N Q 0.066 24 N 0.139 N
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
110 =================================== ============= =========== ============ ============= =========== ============ ============= =========== ============ ============== ============= ========== ========= ======== ============== ============ ============= =============== ==============
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
111
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
112 **Truncation**
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
113
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
114 Signal peptides are found at the start of a protein, so there is limited value in providing the full length sequence, and providing the full sequence slows down the analysis. Furthermore, SignalP has an upper bound on the sequence length it will accept (6000bp). Thus for practical reasons it is useful to truncate the proteins before passing them to SignalP. However, the precise point they are truncated does have a small influence on some score values, and thus to the results.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
115
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
116 **References**
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
117
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
118 Bendtsen, Nielsen, von Heijne, and Brunak.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
119 Improved prediction of signal peptides: SignalP 3.0.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
120 J. Mol. Biol., 340:783-795, 2004.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
121
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
122 Nielsen, Engelbrecht, Brunak and von Heijne.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
123 Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
124 Protein Engineering, 10:1-6, 1997.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
125
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
126 Nielsen and Krogh.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
127 Prediction of signal peptides and signal anchors by a hidden Markov model.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
128 Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology (ISMB 6),
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
129 AAAI Press, Menlo Park, California, pp. 122-130, 1998.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
130
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
131 http://www.cbs.dtu.dk/services/SignalP-3.0/output.php
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
132
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
133 </help>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
134 </tool>