Mercurial > repos > peterjc > tmhmm_and_signalp
comparison tools/protein_analysis/signalp3.xml @ 1:3ff1dcbb9440
Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
author | peterjc |
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date | Tue, 07 Jun 2011 18:04:05 -0400 |
parents | bca9bc7fdaef |
children | f3b373a41f81 |
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0:bca9bc7fdaef | 1:3ff1dcbb9440 |
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1 <tool id="signalp3" name="SignalP 3.0" version="0.0.1"> | 1 <tool id="signalp3" name="SignalP 3.0" version="0.0.3"> |
2 <description>Find signal peptides in protein sequences</description> | 2 <description>Find signal peptides in protein sequences</description> |
3 <command interpreter="python"> | 3 <command interpreter="python"> |
4 signalp3.py $organism $truncate 8 $fasta_file $tabular_file | 4 signalp3.py $organism $truncate 8 $fasta_file $tabular_file |
5 ##I want the number of threads to be a Galaxy config option... | 5 ##I want the number of threads to be a Galaxy config option... |
6 </command> | 6 </command> |
24 <tests> | 24 <tests> |
25 <test> | 25 <test> |
26 <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta"/> | 26 <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta"/> |
27 <param name="organism" value="euk"/> | 27 <param name="organism" value="euk"/> |
28 <param name="truncate" value="0"/> | 28 <param name="truncate" value="0"/> |
29 <output name="tabular_file" file="four_human_proteins.signalp3.tsv" ftype="tabular"/> | 29 <output name="tabular_file" file="four_human_proteins.signalp3.tabular" ftype="tabular"/> |
30 </test> | |
31 <test> | |
32 <param name="fasta_file" value="empty.fasta" ftype="fasta"/> | |
33 <param name="organism" value="euk"/> | |
34 <param name="truncate" value="60"/> | |
35 <output name="tabular_file" file="empty_signalp3.tabular" ftype="tabular"/> | |
36 </test> | |
37 <test> | |
38 <param name="fasta_file" value="empty.fasta" ftype="fasta"/> | |
39 <param name="organism" value="gram+"/> | |
40 <param name="truncate" value="80"/> | |
41 <output name="tabular_file" file="empty_signalp3.tabular" ftype="tabular"/> | |
42 </test> | |
43 <test> | |
44 <param name="fasta_file" value="empty.fasta" ftype="fasta"/> | |
45 <param name="organism" value="gram-"/> | |
46 <param name="truncate" value="0"/> | |
47 <output name="tabular_file" file="empty_signalp3.tabular" ftype="tabular"/> | |
30 </test> | 48 </test> |
31 </tests> | 49 </tests> |
32 <help> | 50 <help> |
33 | 51 |
34 **What it does** | 52 **What it does** |
35 | 53 |
36 This calls the SignalP v3.0 tool for prediction of signal peptides, which uses both a neural network (NN) and Hidden Markmov Model (HMM) to produce two sets of scores. | 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. |
37 | 55 |
38 The input is a FASTA file of protein sequences, and the output is tabular with twenty columns (one row per protein): | 56 The input is a FASTA file of protein sequences, and the output is tabular with twenty columns (one row per protein): |
39 | 57 |
40 * Sequence identifier | 58 * Sequence identifier |
41 * Neural Network (NN) predictions (13 columns) | 59 * Neural Network (NN) predictions (13 columns) |
55 | 73 |
56 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. | 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. |
57 | 75 |
58 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. | 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. |
59 | 77 |
60 The D-score is 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. | 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. |
61 | 79 |
62 For non-secretory proteins all the scores represented in the SignalP3-NN output should ideally be very low. | 80 For non-secretory proteins all the scores represented in the SignalP3-NN output should ideally be very low. |
63 | 81 |
64 **Hidden Markov Model Scores** | 82 **Hidden Markov Model Scores** |
65 | 83 |