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Protocols

Lutefisk specifications

Information


Unique identifier OMICS_02476
Name Lutefisk
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format ASCII, ".dta" files
Operating system Unix/Linux, Mac OS, Windows
Programming languages C
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.0.7
Stability Stable
Maintained Yes

Download


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Versioning


No version available

Maintainer


  • person_outline Richard Johnson

Additional information


http://www.hairyfatguy.com/lutefisk/docs/

Publications for Lutefisk

Lutefisk citations

 (9)
library_books

Peptide de novo sequencing of mixture tandem mass spectra

2016
Proteomics
PMCID: 5297990
PMID: 27329701
DOI: 10.1002/pmic.201500549

[…] arning techniques , , composition restriction by accurate mass measurements , , divide‐and‐conquer , or linear sequencing algorithms , are other methods used. Some well‐known programs are SHERENGA , Lutefisk , NovoHMM , PEAKS , PepNovo , and pNovo .De novo sequencing approaches have recently received more attention due to the growing availability of high mass accuracy instrumentation . The best d […]

call_split

Neuropeptidomics: Mass Spectrometry Based Identification and Quantitation of Neuropeptides

2016
PMCID: 4838524
PMID: 27103886
DOI: 10.5808/GI.2016.14.1.12
call_split See protocol

[…] novo sequencing can be performed manually, the process is labor-intensive and time-consuming. There are several software packages that can perform de novo sequencing directly on MS/MS data, including Lutefisk (http://www.hairyfatguy.com/lutefisk/), Mascot Distiller (Matrix Science), and PEAKS (Bioinformatics Solutions, http://www.bioinformaticssolutions.com/) []. The peptide sequences obtained fro […]

library_books

A Draft Map of Rhesus Monkey Tissue Proteome for Biomedical Research

2015
PLoS One
PMCID: 4431823
PMID: 25974132
DOI: 10.1371/journal.pone.0126243

[…] Alternatively, the de novo peptide sequencing strategy was introduced as a promising methodology for interpretation of LC-MS/MS data from unknown species. However, current software such as DeNoS [], Lutefisk[] and PEAKS[] do not yet support a fully automated search function, so they eventually require much more time than automated database search engines.The term “non-human primate” is used to de […]

library_books

Mass spectrometry based protein identification by integrating de novo sequencing with database searching

2013
BMC Bioinformatics
PMCID: 3549845
PMID: 23369017
DOI: 10.1186/1471-2105-14-S2-S24

[…] derived from peptide fragment ions without recourse to any protein database. Existing de novo sequencing methods can be classified into two categories. For the first category, such as Sherenga [] and Lutefisk [], the problem is projected into graph theory and algorithms used for finding the maximum path in a network topology are applied to achieve identification. In the second category, exemplifie […]

call_split

OpenKnowledge for peer to peer experimentation in protein identification by MS/MS

2011
PMCID: 3377912
PMID: 22192521
DOI: 10.1186/1759-4499-3-3
call_split See protocol

[…] veloped to access and manipulate web servers and/or local programs for MS/MS identification, including algorithms OMSSA and MASCOT subscribed to the role pff_approach, PepNovo Win32 Executable [] and Lutefisk XPv1.0 [] performed the role denovo_approach, and MS-BLAST [] subscribed to the role similarity_search. In this experiment, parameters for MASCOT was set with database NCBI nr, enzyme trypsin […]

library_books

Identification of a novel Plasmopara halstedii elicitor protein combining de novo peptide sequencing algorithms and RACE PCR

2010
Proteome Sci
PMCID: 2881003
PMID: 20459704
DOI: 10.1186/1477-5956-8-24

[…] erform computational identifications automatically. Most algorithms employ a graph-theoretical approach by representing the spectrum with a "spectrum graph" []. Popular examples for this approach are Lutefisk [,] and PepNovo []. Different approaches are used by PEAKS online [,], NovoHMM [], PILOT [] and CompNovo []. For further information, a review of several common de novo algorithms is given el […]

Citations

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Lutefisk institution(s)
Department of Biochemistry, University of Washington, Seattle, WA, USA; Immunex Corporation, Seattle, WA, USA

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