Mercurial > repos > jfb > kinamine_y_for_peptide_shaker

comparison KM Y PS/Kinamine_PS.xml @ 8:0438f8825718 draft

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author jfb
date Tue, 17 Sep 2019 16:18:22 -0400
parents e21ef020d1a6
children 37e9bb9be4bf
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7:5b4bd0d94cdd 8:0438f8825718
32 <help><![CDATA[ 32 <help><![CDATA[
33 Kinamine takes a Distinct Peptide Report and extracts from it all peptides containing a phospho(Y), along with the 7 amino acids N- and C- terminal to the pY in that peptide (assuming they were discovered at a threshold above the given FDR value). This file is the *Substrates* file 33 Kinamine takes a Distinct Peptide Report and extracts from it all peptides containing a phospho(Y), along with the 7 amino acids N- and C- terminal to the pY in that peptide (assuming they were discovered at a threshold above the given FDR value). This file is the *Substrates* file
34 Additionally, all discovered peptides are assumed to have come from a protein. For every phospho(Y) peptide, KinaMine takes the associated protein accession number, searches the FASTA file for that accession number and returns the amino acid percent composition of the protein(s) which that peptide came from. This file is the *Substrate Background Frequency* file 34 Additionally, all discovered peptides are assumed to have come from a protein. For every phospho(Y) peptide, KinaMine takes the associated protein accession number, searches the FASTA file for that accession number and returns the amino acid percent composition of the protein(s) which that peptide came from. This file is the *Substrate Background Frequency* file
35 This tool is intended to be used in conjunction with Negative Motif Finder and Kinatest, the three together creating a GalaxyP version of the KINATEST-ID workbook. 35 This tool is intended to be used in conjunction with Negative Motif Finder and Kinatest, the three together creating a GalaxyP version of the KINATEST-ID workbook.
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37 java -Djava.awt.headless=true -jar JavaApplication4.jar psm.tabular reference.fasta outputs 0.5 output
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37 =========== 39 ===========
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39 Inputs 41 Inputs
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41 PSM Phosphorylation Report: This is the file that Peptide Shaker can creates after a search is run using SearchGUI 43 PSM Phosphorylation Report: This is the file that Peptide Shaker can creates after a search is run using SearchGUI