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DirecTag
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Tagging MS/MS without abstraction
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Sequence tagging is designed to complement database search tools like MyriMatch by providing partial explanations for experimental data. The partial explanations (tags) can later be used to reconcile against a protein database, usually allowing for modifications and/or mutations because of the extreme filtration of the search space by the tags. DirecTag has been tested with many instrument types. It can parallelize its task across multiple processors via threading or compute nodes via the Message Passing Interface.
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Latest stable release:
Download:
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06/11/2008
Documentation
Changelog
Windows 2000/XP/Vista
Source code (tarball)
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MyriMatch
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Identifying MS/MS through database search
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MyriMatch is a tool designed to take experimental data from shotgun proteomics experiments and compare those spectra against sequences in a known database of proteins. Whether the program is being run in a single-computer environment or across an entire cluster of processing nodes, it is able to optimally divide work in a much more efficient way than many other database search programs. This is because it only generates candidate sequences from the known database once for the entire set of spectra instead of once for every spectrum. Thus, for each candidate sequence generated, it is compared against every spectrum. The spectra keep a certain (user-defined) number of candidate sequences that had the highest scores.
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Latest stable release:
Download:
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06/05/2009
Documentation
Changelog
Windows 2000/XP/Vista
Source code (tarball)
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IDPicker
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Filtering, assembling, and reporting parsimonious protein identifications
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Protein assembly is the process of transforming raw peptide identifications into confident protein identifications. IDPicker infers score thresholds to achieve target false discovery rates (FDR) among peptide identifications. The software can remove artifactual proteins for more parsimonious protein reporting. IDPicker's HTML protein reports cluster indiscernible proteins and those that share peptides, making it far easier to learn the biological lessons presented by each sample. It applies a user-specified experimental hierarchy to collections of peptide identifications and enables users to track the number of spectra or peptides observed for a given protein across multiple experiments.
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Latest stable release:
Download:
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03/30/2009
Documentation
Changelog
Windows 2000/XP/Vista
Source code (tarball)
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