comparison KM Y PS/Kinamine_PS.xml @ 11:37e9bb9be4bf draft

Uploaded

10:94167015c3d1

    <help><![CDATA[
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
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
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.

java -Djava.awt.headless=true -jar JavaApplication4.jar psm.tabular reference.fasta outputs 0.5 output

===========

Inputs

PSM Phosphorylation Report: This is the file that Peptide Shaker can creates after a search is run using SearchGUI

KinaMine then extracts only the phospho-Y peptides and the proteins they came from.  Negative Motif finder finds all pY-containing peptides that could have been discovered but weren't.  Kinatest then uses all this data to discover candidate substrates which will be specific for the given kinase and no others.  From the discovered substrates, a biosensor can be made.


    ]]></help>
    <citations>
        <citation type="doi">10.1021/ja507164a</citation>
    </citations>
</tool>

11:37e9bb9be4bf

    <help><![CDATA[
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
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
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.

===========

Inputs

PSM Phosphorylation Report: This is the file that Peptide Shaker can creates after a search is run using SearchGUI

KinaMine then extracts only the phospho-Y peptides and the proteins they came from.  Negative Motif finder finds all pY-containing peptides that could have been discovered but weren't.  Kinatest then uses all this data to discover candidate substrates which will be specific for the given kinase and no others.  From the discovered substrates, a biosensor can be made.


    ]]></help>
    <citations>
        <citation type="doi">10.1074/mcp.RA118.001111</citation>
    </citations>
</tool>