Available Search Engines¶
Protein Database Search Engines¶
MS Amanda¶
Available MS Amanda versions, starting with the newest version:
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class
ursgal.wrappers.msamanda_2_0_0_14665.
msamanda_2_0_0_14665
(*args, **kwargs)¶ MSAmanda 2_0_0_14665 UNode
Import functions from msamanda_2_0_0_9695
This third party engine can be downloaded from: https://ms.imp.ac.at/?goto=msamanda
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class
ursgal.wrappers.msamanda_2_0_0_13723.
msamanda_2_0_0_13723
(*args, **kwargs)¶ MSAmanda 2_0_0_13723 UNode
Import functions from msamanda_2_0_0_9695
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class
ursgal.wrappers.msamanda_2_0_0_11219.
msamanda_2_0_0_11219
(*args, **kwargs)¶ MSAmanda 2_0_0_11219 UNode
Import functions from msamanda_2_0_0_9695
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class
ursgal.wrappers.msamanda_2_0_0_10695.
msamanda_2_0_0_10695
(*args, **kwargs)¶ MSAmanda 2_0_0_9706 UNode
Import functions from msamanda_2_0_0_9695
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class
ursgal.wrappers.msamanda_2_0_0_9706.
msamanda_2_0_0_9706
(*args, **kwargs)¶ MSAmanda 2_0_0_9706 UNode
Import functions from msamanda_2_0_0_9695
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class
ursgal.wrappers.msamanda_2_0_0_9695.
msamanda_2_0_0_9695
(*args, **kwargs)¶ MSAmanda 2_0_0_9695 UNode Parameter options at http://ms.imp.ac.at/inc/pd-nodes/msamanda/Manual%20MS%20Amanda%20Standalone.pdf
Note: Please download and install MSAmanda manually from http://ms.imp.ac.at/?goto=msamanda
Reference: Dorfer V, Pichler P, Stranzl T, Stadlmann J, Taus T, Winkler S, Mechtler K. (2014) MS Amanda, a universal identification algorithm optimized for high accuracy tandem mass spectra.
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postflight
()¶ Convert .tsv result files to .csv
-
preflight
()¶ Formatting the command line via self.params
Settings file is created in the output folder and added to self.created_tmp_files (can be deleted)
Returns: self.params(dict)
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-
class
ursgal.wrappers.msamanda_1_0_0_7504.
msamanda_1_0_0_7504
(*args, **kwargs)¶ MSAmanda 1_0_0_7504 UNode
Import functions from msamanda_1_0_0_5243
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class
ursgal.wrappers.msamanda_1_0_0_7503.
msamanda_1_0_0_7503
(*args, **kwargs)¶ MSAmanda 1_0_0_7503 UNode
Import functions from msamanda_1_0_0_5243
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class
ursgal.wrappers.msamanda_1_0_0_5243.
msamanda_1_0_0_5243
(*args, **kwargs)¶ MSAmanda 1_0_0_5243 UNode Parameter options at http://ms.imp.ac.at/inc/pd-nodes/msamanda/Manual%20MS%20Amanda%20Standalone.pdf
Reference: Dorfer V, Pichler P, Stranzl T, Stadlmann J, Taus T, Winkler S, Mechtler K. (2014) MS Amanda, a universal identification algorithm optimized for high accuracy tandem mass spectra.
-
postflight
()¶ Convert .tsv result files to .csv
-
preflight
()¶ Formatting the command line via self.params
Settings file is created in the output folder and added to self.created_tmp_files (can be deleted)
Returns: self.params(dict)
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-
class
ursgal.wrappers.msamanda_1_0_0_5242.
msamanda_1_0_0_5242
(*args, **kwargs)¶ MSAmanda 1_0_0_5242 UNode
Import functions from msamanda_1_0_0_5243
MS-GF+¶
Available MS-GF+ versions, starting with the newest version:
-
class
ursgal.wrappers.msgfplus_v2019_07_03.
msgfplus_v2019_07_03
(*args, **kwargs)¶ MSGF+ UNode Parameter options at https://omics.pnl.gov/software/ms-gf
- Reference:
- Kim S, Mischerikow N, Bandeira N, Navarro JD, Wich L, Mohammed S, Heck AJ, Pevzner PA. (2010) The Generating Function of CID, ETD, and CID/ETD Pairs of Tandem Mass Spectra: Applications to Database Search.
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postflight
()¶ This can be/is overwritten by the engine uNode class
-
preflight
()¶ Formatting the command line via self.params
Modifications file will be created in the output folder
Returns: self.params Return type: dict
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class
ursgal.wrappers.msgfplus_v2019_04_18.
msgfplus_v2019_04_18
(*args, **kwargs)¶ MSGF+ UNode Parameter options at https://omics.pnl.gov/software/ms-gf
- Reference:
- Kim S, Mischerikow N, Bandeira N, Navarro JD, Wich L, Mohammed S, Heck AJ, Pevzner PA. (2010) The Generating Function of CID, ETD, and CID/ETD Pairs of Tandem Mass Spectra: Applications to Database Search.
Import node for version 2016_09_16
-
class
ursgal.wrappers.msgfplus_v2019_01_22.
msgfplus_v2019_01_22
(*args, **kwargs)¶ MSGF+ UNode Parameter options at https://omics.pnl.gov/software/ms-gf
- Reference:
- Kim S, Mischerikow N, Bandeira N, Navarro JD, Wich L, Mohammed S, Heck AJ, Pevzner PA. (2010) The Generating Function of CID, ETD, and CID/ETD Pairs of Tandem Mass Spectra: Applications to Database Search.
Import node for version 2016_09_16
-
class
ursgal.wrappers.msgfplus_v2018_09_12.
msgfplus_v2018_09_12
(*args, **kwargs)¶ MSGF+ UNode Parameter options at https://omics.pnl.gov/software/ms-gf
- Reference:
- Kim S, Mischerikow N, Bandeira N, Navarro JD, Wich L, Mohammed S, Heck AJ, Pevzner PA. (2010) The Generating Function of CID, ETD, and CID/ETD Pairs of Tandem Mass Spectra: Applications to Database Search.
Import node for version 2016_09_16
-
class
ursgal.wrappers.msgfplus_v2018_06_28.
msgfplus_v2018_06_28
(*args, **kwargs)¶ MSGF+ UNode Parameter options at https://omics.pnl.gov/software/ms-gf
- Reference:
- Kim S, Mischerikow N, Bandeira N, Navarro JD, Wich L, Mohammed S, Heck AJ, Pevzner PA. (2010) The Generating Function of CID, ETD, and CID/ETD Pairs of Tandem Mass Spectra: Applications to Database Search.
Import node for version 2016_09_16
-
class
ursgal.wrappers.msgfplus_v2018_01_30.
msgfplus_v2018_01_30
(*args, **kwargs)¶ MSGF+ UNode Parameter options at https://omics.pnl.gov/software/ms-gf
- Reference:
- Kim S, Mischerikow N, Bandeira N, Navarro JD, Wich L, Mohammed S, Heck AJ, Pevzner PA. (2010) The Generating Function of CID, ETD, and CID/ETD Pairs of Tandem Mass Spectra: Applications to Database Search.
Import node for version 2016_09_16
-
class
ursgal.wrappers.msgfplus_v2017_01_27.
msgfplus_v2017_01_27
(*args, **kwargs)¶ MSGF+ UNode Parameter options at https://omics.pnl.gov/software/ms-gf
- Reference:
- Kim S, Mischerikow N, Bandeira N, Navarro JD, Wich L, Mohammed S, Heck AJ, Pevzner PA. (2010) The Generating Function of CID, ETD, and CID/ETD Pairs of Tandem Mass Spectra: Applications to Database Search.
Import node for version 2016_09_16
-
class
ursgal.wrappers.msgfplus_v2016_09_16.
msgfplus_v2016_09_16
(*args, **kwargs)¶ MSGF+ UNode Parameter options at https://omics.pnl.gov/software/ms-gf
- Reference:
- Kim S, Mischerikow N, Bandeira N, Navarro JD, Wich L, Mohammed S, Heck AJ, Pevzner PA. (2010) The Generating Function of CID, ETD, and CID/ETD Pairs of Tandem Mass Spectra: Applications to Database Search.
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postflight
()¶ This can be/is overwritten by the engine uNode class
-
preflight
()¶ Formatting the command line via self.params
Modifications file will be created in the output folder
Returns: self.params Return type: dict
-
class
ursgal.wrappers.msgfplus_v9979.
msgfplus_v9979
(*args, **kwargs)¶ MSGF+ UNode Parameter options at https://bix-lab.ucsd.edu/pages/viewpage.action?pageId=13533355
Reference: Kim S, Mischerikow N, Bandeira N, Navarro JD, Wich L, Mohammed S, Heck AJ, Pevzner PA. (2010) The Generating Function of CID, ETD, and CID/ETD Pairs of Tandem Mass Spectra: Applications to Database Search.
-
preflight
()¶ Formatting the command line via self.params
Modifications file will be created in the output folder
Returns: self.params Return type: dict
-
MSFragger¶
Available MSFragger versions, starting with the newest version:
-
class
ursgal.wrappers.msfragger_3_0.
msfragger_3_0
(*args, **kwargs)¶ MSFragger unode
Note
Please download and install MSFragger manually from http://www.nesvilab.org/software.html
Reference: Kong, A. T., Leprevost, F. V, Avtonomov, D. M., Mellacheruvu, D., and Nesvizhskii, A. I. (2017) MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics. Nature Methods 14
Note
Addition of user amino acids not implemented yet. Only mzML search possible at the moment. The mgf file can still be passed to the node, but the mzML has to be in the same folder as the mgf.
Warning
Still in testing phase! Metabolic labeling based 15N search may still be errorprone. Use with care!
-
postflight
()¶ Reads MSFragger tsv output and write final csv output file.
- Adds:
- Raw data location, since this can not be added later
- Converts masses in Da to m/z (could be done in unify_csv)
-
preflight
()¶ Formatting the command line and writing the param input file via self.params
Returns: self.params Return type: dict
-
-
class
ursgal.wrappers.msfragger_2_3.
msfragger_2_3
(*args, **kwargs)¶ MSFragger unode
Note
Please download and install MSFragger manually from http://www.nesvilab.org/software.html
Reference: Kong, A. T., Leprevost, F. V, Avtonomov, D. M., Mellacheruvu, D., and Nesvizhskii, A. I. (2017) MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics. Nature Methods 14
Note
Addition of user amino acids not implemented yet. Only mzML search possible at the moment. The mgf file can still be passed to the node, but the mzML has to be in the same folder as the mgf.
Warning
Still in testing phase! Metabolic labeling based 15N search may still be errorprone. Use with care!
-
class
ursgal.wrappers.msfragger_20190628.
msfragger_20190628
(*args, **kwargs)¶ MSFragger unode
Note
Please download and install MSFragger manually from http://www.nesvilab.org/software.html
Reference: Kong, A. T., Leprevost, F. V, Avtonomov, D. M., Mellacheruvu, D., and Nesvizhskii, A. I. (2017) MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics. Nature Methods 14
Note
Addition of user amino acids not implemented yet. Only mzML search possible at the moment. The mgf file can still be passed to the node, but the mzML has to be in the same folder as the mgf.
Warning
Still in testing phase! Metabolic labeling based 15N search may still be errorprone. Use with care!
-
postflight
()¶ Reads MSFragger tsv output and write final csv output file.
- Adds:
- Raw data location, since this can not be added later
- Converts masses in Da to m/z (could be done in unify_csv)
-
preflight
()¶ Formatting the command line and writing the param input file via self.params
Returns: self.params Return type: dict
-
-
class
ursgal.wrappers.msfragger_20190222.
msfragger_20190222
(*args, **kwargs)¶ MSFragger unode
Note
Please download and install MSFragger manually from http://www.nesvilab.org/software.html
Reference: Kong, A. T., Leprevost, F. V, Avtonomov, D. M., Mellacheruvu, D., and Nesvizhskii, A. I. (2017) MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics. Nature Methods 14
Note
Addition of user amino acids not implemented yet. Only mzML search possible at the moment. The mgf file can still be passed to the node, but the mzML has to be in the same folder as the mgf.
Warning
Still in testing phase! Metabolic labeling based 15N search may still be errorprone. Use with care!
-
class
ursgal.wrappers.msfragger_20171106.
msfragger_20171106
(*args, **kwargs)¶ MSFragger unode
Note
Please download and install MSFragger manually from http://www.nesvilab.org/software.html
Reference: Kong, A. T., Leprevost, F. V, Avtonomov, D. M., Mellacheruvu, D., and Nesvizhskii, A. I. (2017) MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics. Nature Methods 14
Note
Addition of user amino acids not implemented yet. Only mzML search possible at the moment. The mgf file can still be passed to the node, but the mzML has to be in the same folder as the mgf.
Warning
Still in testing phase! Metabolic labeling based 15N search may still be errorprone. Use with care!
-
class
ursgal.wrappers.msfragger_20170103.
msfragger_20170103
(*args, **kwargs)¶ MSFragger unode
Note
Please download and install MSFragger manually from http://www.nesvilab.org/software.html
Reference: Kong, A. T., Leprevost, F. V, Avtonomov, D. M., Mellacheruvu, D., and Nesvizhskii, A. I. (2017) MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics. Nature Methods 14
Note
Addition of user amino acids not implemented yet. Only mzML search possible at the moment. The mgf file can still be passed to the node, but the mzML has to be in the same folder as the mgf.
Warning
Still in testing phase! Metabolic labeling based 15N search may still be errorprone. Use with care!
-
postflight
()¶ Reads MSFragger tsv output and write final csv output file.
- Adds:
- Raw data location, since this can not be added later
- Converts masses in Da to m/z (could be done in unify_csv)
-
preflight
()¶ Formatting the command line and writing the param input file via self.params
Returns: self.params Return type: dict
-
MODa¶
Available MODa versions, starting with the newest version:
-
class
ursgal.wrappers.moda_v1_62.
moda_v1_62
(*args, **kwargs)¶ MODa UNode Check http://prix.hanyang.ac.kr/download/moda.jsp for download, new versions and contact information
Reference: Na S, Bandeira N, Paek E. (2012) Fast multi-blind modification search through tandem mass spectrometry.
-
postflight
()¶ Rewrite ModA output .tsv into .csv so that it can be unified
-
preflight
()¶ Formatting the command line via self.params
Returns: self.params Return type: dict
-
-
class
ursgal.wrappers.moda_v1_61.
moda_v1_61
(*args, **kwargs)¶ MODa UNode Check http://prix.hanyang.ac.kr/download/moda.jsp for download, new versions and contact information
Reference: Na S, Bandeira N, Paek E. (2012) Fast multi-blind modification search through tandem mass spectrometry.
-
postflight
()¶ Rewrite ModA output .tsv into .csv so that it can be unified
-
preflight
()¶ Formatting the command line via self.params
Returns: self.params Return type: dict
-
-
class
ursgal.wrappers.moda_v1_51.
moda_v1_51
(*args, **kwargs)¶ MODa UNode Check http://prix.hanyang.ac.kr/download/moda.jsp for download, new versions and contact information
Reference: Na S, Bandeira N, Paek E. (2012) Fast multi-blind modification search through tandem mass spectrometry.
-
postflight
()¶ Rewrite ModA output .tsv into .csv so that it can be unified
-
preflight
()¶ Formatting the command line via self.params
Returns: self.params Return type: dict
-
MyriMatch¶
-
class
ursgal.wrappers.myrimatch_2_1_138.
myrimatch_2_1_138
(*args, **kwargs)¶ Myrimatch UNode
Myrimatch options: http://forge.fenchurch.mc.vanderbilt.edu/scm/viewvc.php/checkout/trunk/doc/index.html?root=myrimatch
Reference: Tabb DL, Fernando CG, Chambers MC. (2007) MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis.
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postflight
()¶ renaming MyriMatch’s output file to our desired output file name
-
preflight
()¶ Formatting the command line
-
write_param_file
()¶ Writes a file containing all parameters for the search
-
-
class
ursgal.wrappers.myrimatch_2_2_140.
myrimatch_2_2_140
(*args, **kwargs)¶ Myrimatch UNode
Import functions from myrimatch_2_1_138
TagGraph¶
This open modification search engine uses de novo search engine results but takes a protein database into account as well.
-
class
ursgal.wrappers.tag_graph_1_8_0.
tag_graph_1_8_0
(*args, **kwargs)¶ TagGraph unode For further information see https://sourceforge.net/projects/taggraph/
Note
Please download and install MSFragger manually from http://www.nesvilab.org/software.html
Reference: Devabhaktuni, A.; Lin, S.; Zhang, L.; Swaminathan, K.; Gonzalez, CG.; Olsson, N.; Pearlman, SM.; Rawson, K.; Elias, JE. (2019) TagGraph reveals vast protein modification landscapes from large tandem mass spectrometry datasets. Nat Biotechnol. 37(4)
-
postflight
()¶ Reads TagGraph tdv output and write final csv output file.
-
preflight
()¶ Formatting the command line and writing two param input files via self.params
Returns: self.params Return type: dict
-
OMSSA¶
-
class
ursgal.wrappers.omssa_2_1_9.
omssa_2_1_9
(*args, **kwargs)¶ omssa_2_1_9 UNode
Parameter options at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/asn_spec/omssa.asn.html
OMSSA 2.1.9 parameters at http://proteomicsresource.washington.edu/protocols06/omssa.php
Reference: Geer LY, Markey SP, Kowalak JA, Wagner L, Xu M, Maynard DM, Yang X, Shi W, Bryant SH (2004) Open Mass Spectrometry Search Algorithm.
-
postflight
()¶ Will correct the OMSSA headers and add the column retention time to the csv file
-
preflight
()¶ Formatting the command line via self.params
unimod Modifications are translated to OMSSA modifications
Returns: self.params(dict)
-
PIPI¶
Available PIPI versions, starting with the newest version:
-
class
ursgal.wrappers.pipi_1_4_6.
pipi_1_4_6
(*args, **kwargs)¶ Unode for PIPI: PTM-Invariant Peptide Identification For furhter information see: http://bioinformatics.ust.hk/pipi.html
Note
Please download and extract PIPI manually from http://bioinformatics.ust.hk/pipi.html
Reference: Yu, F., Li, N., Yu, W. (2016) PIPI: PTM-Invariant Peptide Identification Using Coding Method. J Prot Res 15(12)
-
class
ursgal.wrappers.pipi_1_4_5.
pipi_1_4_5
(*args, **kwargs)¶ Unode for PIPI: PTM-Invariant Peptide Identification For furhter information see: http://bioinformatics.ust.hk/pipi.html
Note
Please download and extract PIPI manually from http://bioinformatics.ust.hk/pipi.html
Reference: Yu, F., Li, N., Yu, W. (2016) PIPI: PTM-Invariant Peptide Identification Using Coding Method. J Prot Res 15(12)
-
postflight
()¶ This can be/is overwritten by the engine uNode class
-
preflight
()¶ Formatting the command line and writing the param input file via self.params
Returns: self.params Return type: dict
-
X!Tandem¶
Available X!Tandem versions, starting with the newest version:
-
class
ursgal.wrappers.xtandem_alanine.
xtandem_alanine
(*args, **kwargs)¶ X!Tandem UNode Parameter options at http://www.thegpm.org/TANDEM/api/
Reference: Craig R, Beavis RC. (2004) TANDEM: matching proteins with tandem mass spectra.
-
class
ursgal.wrappers.xtandem_vengeance.
xtandem_vengeance
(*args, **kwargs)¶ X!Tandem UNode Parameter options at http://www.thegpm.org/TANDEM/api/
Reference: Craig R, Beavis RC. (2004) TANDEM: matching proteins with tandem mass spectra.
-
format_templates
()¶ Returns formatted X!Tandem input files
The formating is taken from self.params
Returns: keys are the names of the three templates (15N-masses.xml, taxonomy.xml, input.xml) Return type: dict
-
postflight
()¶ This can be/is overwritten by the engine uNode class
-
preflight
()¶ Formatting the command line via self.params
Input files from format_templates are created in the output folder and added to self.created_tmp_files (can be deleted)
Returns: self.params Return type: dict
-
-
class
ursgal.wrappers.xtandem_piledriver.
xtandem_piledriver
(*args, **kwargs)¶ X!Tandem UNode Parameter options at http://www.thegpm.org/TANDEM/api/
Reference: Craig R, Beavis RC. (2004) TANDEM: matching proteins with tandem mass spectra.
-
format_templates
()¶ Returns formatted X!Tandem input files
The formating is taken from self.params
Returns: keys are the names of the three templates (15N-masses.xml, taxonomy.xml, input.xml) Return type: dict
-
postflight
()¶ This can be/is overwritten by the engine uNode class
-
preflight
()¶ Formatting the command line via self.params
Input files from format_templates are created in the output folder and added to self.created_tmp_files (can be deleted)
Returns: self.params Return type: dict
-
-
class
ursgal.wrappers.xtandem_sledgehammer.
xtandem_sledgehammer
(*args, **kwargs)¶ X!Tandem UNode Parameter options at http://www.thegpm.org/TANDEM/api/
Reference: Craig R, Beavis RC. (2004) TANDEM: matching proteins with tandem mass spectra.
-
format_templates
()¶ Returns formatted X!Tandem input files
The formating is taken from self.params
Returns: keys are the names of the three templates (15N-masses.xml, taxonomy.xml, input.xml) Return type: dict
-
postflight
()¶ This can be/is overwritten by the engine uNode class
-
preflight
()¶ Formatting the command line via self.params
Input files from format_templates are created in the output folder and added to self.created_tmp_files (can be deleted)
Returns: self.params Return type: dict
-
-
class
ursgal.wrappers.xtandem_jackhammer.
xtandem_jackhammer
(*args, **kwargs)¶
-
class
ursgal.wrappers.xtandem_cyclone_2010.
xtandem_cyclone_2010
(*args, **kwargs)¶
De Novo Search Engines¶
DeepNovo¶
Available DeepNovo versions, starting with the newest version:
-
class
ursgal.wrappers.deepnovo_pointnovo.
deepnovo_pointnovo
(*args, **kwargs)¶ PointNovo UNode pytorch re-implementation of DeepNovo For further information, see https://github.com/volpato30/PointNovo/
Reference: Tran, N.H.; Zhang, X.; Xin, L.; Shan, B.; Li, M. (2017) De novo peptide sequencing by deep learning. PNAS 114 (31)
-
postflight
()¶ Reformats the DeepNovo output file
-
preflight
()¶ Create deepnovo_config.py file and format command line via self.params
Returns: self.params Return type: dict
-
-
class
ursgal.wrappers.deepnovo_0_0_1.
deepnovo_0_0_1
(*args, **kwargs)¶ DeepNovo UNode For further information, see https://github.com/nh2tran/DeepNovo
Note
Please download manually from https://github.com/StSchulze/DeepNovo?organization=StSchulze&organization=StSchulze or using git clone https://github.com/StSchulze/DeepNovo.git and download the model from https://drive.google.com/open?id=0By9IxqHK5MdWalJLSGliWW1RY2c
Reference: Tran, N.H.; Zhang, X.; Xin, L.; Shan, B.; Li, M. (2017) De novo peptide sequencing by deep learning. PNAS 114 (31)
-
postflight
()¶ Reformats the DeepNovo output file
-
preflight
()¶ Create deepnovo_config.py file and format command line via self.params
Returns: self.params Return type: dict
-
Novor¶
Available Novor versions, starting with the newest version:
-
class
ursgal.wrappers.novor_1_05.
novor_1_05
(*args, **kwargs)¶ Novor UNode Parameter options at http://rapidnovor.com/
Reference: Bin Ma (2015) Novor: Real-Time Peptide de Novo Sequencing Software. J Am Soc Mass Spectrom 26 (11)
Import node for version novor_1_1beta
-
postflight
()¶ Reformats the Novor output file
-
preflight
()¶ Formatting the command line via self.params
Params.txt file will be created in the output folder
Returns: self.params Return type: dict
-
-
class
ursgal.wrappers.novor_1_1beta.
novor_1_1beta
(*args, **kwargs)¶ Novor UNode Parameter options at http://rapidnovor.com/
Reference: Bin Ma (2015) Novor: Real-Time Peptide de Novo Sequencing Software.
-
postflight
()¶ Reformats the Novor output file
-
preflight
()¶ Formatting the command line via self.params
Params.txt file will be created in the output folder
Returns: self.params Return type: dict
-
PepNovo¶
-
class
ursgal.wrappers.pepnovo_3_1.
pepnovo_3_1
(*args, **kwargs)¶ PepNovo v3.1 UNode http://proteomics.ucsd.edu/Software/PepNovo/
Reference: Ari M. Frank, Mikhail M. Savitski, Michael L. Nielsen, Roman A. Zubarev, and Pavel A. Pevzner (2007) De Novo Peptide Sequencing and Identification with Precision Mass Spectrometry, J. Proteome Res. 6:114-123.
-
postflight
()¶ Reformats the PepNovo output file
-
preflight
()¶ Formatting the command line via self.params
Returns: self.params Return type: dict
-
pNovo¶
-
class
ursgal.wrappers.pnovo_3_1_3.
pnovo_3_1_3
(*args, **kwargs)¶ Unode for pNovo 3.1.3 For furhter information see: http://pfind.ict.ac.cn/software/pNovo/
Note
Please download pNovo 3.1.3 manually from http://pfind.ict.ac.cn/software/pNovo/#Downloads
Reference: Yang, H; Chi, H; Zhou, W; Zeng, WF; He, K; Liu, C; Sun, RX; He, SM. (2017) Open-pNovo: De Novo Peptide Sequencing with Thousands of Protein Modifications. J Proteome Res. 16(2)
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postflight
()¶ This can be/is overwritten by the engine uNode class
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preflight
()¶ Formatting the command line and writing the param input file via self.params
Returns: self.params Return type: dict
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Cross Link Search Engines¶
Kojak¶
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class
ursgal.wrappers.kojak_1_5_3.
kojak_1_5_3
(*args, **kwargs)¶ Kojak UNode Parameter options at http://www.kojak-ms.org/param/index.html
Reference: Hoopmann MR, Zelter A, Johnson RS, Riffle M, Maccoss MJ, Davis TN, Moritz RL (2015) Kojak: Efficient analysis of chemically cross-linked protein complexes. J Proteome Res 14: 2190-198
Note
Kojak has to be installed manually at the moment! Use folder name: ‘kojak_1_5_3’ in the resources folder.
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format_templates
()¶ Returns formatted input files as a dict.
The standard parametern file is used and adjustes.
Returns: keys are the names of the parametern template file Return type: dict
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postflight
()¶ Move the result files to the Kojak folder, since the output files can not be specified manually.
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preflight
()¶ Formatting the command line via self.params
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Glycosylation Search Engines¶
pGlyco¶
Available pGlyci versions, starting with the newest version:
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class
ursgal.wrappers.pglyco_db_2_2_2.
pglyco_db_2_2_2
(*args, **kwargs)¶ Unode for pGlyco 2.2.2 For furhter information see: https://github.com/pFindStudio/pGlyco2
Note
Please download pGlyco 2.2.2 manually from https://github.com/pFindStudio/pGlyco2
Reference: Liu MQ, Zeng WF,, Fang P, Cao WQ, Liu C, Yan GQ, Zhang Y, Peng C, Wu JQ, Zhang XJ, Tu HJ, Chi H, Sun RX, Cao Y, Dong MQ, Jiang BY, Huang JM, Shen HL, Wong CCL, He SM, Yang PY. (2017) pGlyco 2.0 enables precision N-glycoproteomics with comprehensive quality control and one-step mass spectrometry for intact glycopeptide identification. Nat Commun 8(1)
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class
ursgal.wrappers.pglyco_db_2_2_0.
pglyco_db_2_2_0
(*args, **kwargs)¶ Unode for pGlyco 2.2.0 For furhter information see: https://github.com/pFindStudio/pGlyco2
Note
Please download pGlyco 2.2.0 manually from https://github.com/pFindStudio/pGlyco2
Reference: Liu MQ, Zeng WF,, Fang P, Cao WQ, Liu C, Yan GQ, Zhang Y, Peng C, Wu JQ, Zhang XJ, Tu HJ, Chi H, Sun RX, Cao Y, Dong MQ, Jiang BY, Huang JM, Shen HL, Wong CCL, He SM, Yang PY. (2017) pGlyco 2.0 enables precision N-glycoproteomics with comprehensive quality control and one-step mass spectrometry for intact glycopeptide identification. Nat Commun 8(1)
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postflight
()¶ This can be/is overwritten by the engine uNode class
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preflight
()¶ Formatting the command line and writing the param input file via self.params
Returns: self.params Return type: dict
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