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Peptide freeware
 

Peptide

Added: October 08, 2010 | Visits: 655

Peptide::Pubmed Peptide::Pubmed is a Perl module that can extract peptide sequences from MEDLINE article abstracts. SYNOPSIS use Peptide::Pubmed; $parser = Peptide::Pubmed->new; $in = { PMID => q[15527327], Author => q[Doe JJ, Smith Q], Journal => q[J Biological Foo. 2004;8(2):123-30.], Title => q[Foo,... Platforms: *nix

License: Freeware Size: 358.4 KB Download (75): Peptide::Pubmed Download

Added: July 06, 2010 | Visits: 660

MassSpec::ViewSpectrum::RealVsHypPeptide MassSpec::ViewSpectrum::RealVsHypPeptide is a Perl module to view a real mass spectrum on the same graph as a hypothetical spectrum generated by fragmenting a peptide in silico. SYNOPSIS use MassSpec::ViewSpectrum::RealVsHypPeptide; open GRAPHIC, ">mygraphic.png" or die "Unable to open... Platforms: *nix

License: Freeware Size: 8.19 KB Download (70): MassSpec::ViewSpectrum::RealVsHypPeptide Download

Released: July 19, 2012  |  Added: July 19, 2012 | Visits: 247

msInspect msInspect allows you to process and view mass spectrometry (MS1) data in an mzXML file. You can use msInspect's built-in tools to inspect data, identify peptide features, generate peptide arrays using data from multiple runs, and export data to external applications for further analysis and... Platforms: Windows

License: Freeware Download (50): msInspect Download

Released: June 26, 2012  |  Added: June 26, 2012 | Visits: 313

iPiG iPiG targets the integration of peptide spectrum matches (PSMs) from mass spectrometry (MS) peptide identifications into genomic visualisations provided by genome browser such as the UCSC genome browser (http://genome.ucsc.edu/). iPiG takes PSMs from the MS standard format mzIdentML (*.mzid) or... Platforms: Windows, Mac, Linux

License: Freeware Size: 1.48 MB Download (27): iPiG Download

Released: December 06, 2012  |  Added: December 06, 2012 | Visits: 213

LutefiskXP LutefiskXP is ANSI C compliant software used to perform de novo peptide sequencing from tandem mass spectra. Platforms: Windows, Mac, Solaris

License: Freeware Size: 772.88 KB Download (27): LutefiskXP Download

Released: July 02, 2012  |  Added: July 02, 2012 | Visits: 269

Molevolve Molevolve is a Java library for running a Genetic Algorithm to model the 3-dimensional structures of peptide chains from amino-acid sequences. Client code can specify its own peptide chain model, fitness functions and GA operations. Requires JDK 1.5. Platforms: Windows, Mac, Linux

License: Freeware Size: 1.98 MB Download (29): Molevolve Download

Released: December 01, 2012  |  Added: December 01, 2012 | Visits: 218

PepArML PepArML: An unsupervised, model-free, combining peptide identification arbiter for tandem mass spectra via machine learning. Platforms: Mac, BSD, Linux

License: Freeware Size: 433.76 MB Download (27): PepArML Download

Released: December 06, 2012  |  Added: December 06, 2012 | Visits: 138

prot3d prot3d is aimed to get three-dimensional folding possibilities of a peptide given its aminoacid sequence. Platforms: Windows, Mac, Linux

License: Freeware Size: 4.82 MB Download (27): prot3d Download

Added: January 25, 2010 | Visits: 487

MassSpec::CUtilities MassSpec::CUtilities is a Perl extension containing C utilities for use in mass spectrometry. SYNOPSIS MassSpec::CUtilities is an XS module so theres a chance that you or your target user might not get it to install cleanly on the target system; therefore its recommended to make its presence... Platforms: *nix

License: Freeware Size: 16.38 KB Download (70): MassSpec::CUtilities Download

Added: January 25, 2010 | Visits: 730

Serial Cloner Serial Cloner is a light molecular biology software. Serial Cloner reads and write DNA Strider-compatible files and import and export files in the universal FASTA format (as well as in pDRAW32 format). Powerful graphical display tools and simple interfaces help the analysis and construction steps... Platforms: Mac

License: Freeware Download (84): Serial Cloner Download

Released: September 03, 2012  |  Added: September 03, 2012 | Visits: 273

Insilicos Cloud Army Platform for parallel computation in the Amazon cloud, including machine learning ensembles written in R for computational biology and other areas of scientific research. Home to MR-Tandem, a hadoop-enabled fork of X!Tandem peptide search engine. Platforms: Windows, Mac, Linux

License: Freeware Size: 764.13 KB Download (27): Insilicos Cloud Army Download

Released: December 21, 2012  |  Added: December 21, 2012 | Visits: 289

Proteomic Mass Spectrometer Interface A Mass Spectrometer B and Y ion labeling software for proteomics researchers. Peptide sequences can be read from a library and b and y ions will be calculated and sequence can be manipulated by the user (chem. mod. or amino acid mod.) Platforms: Windows, Mac, Linux

License: Freeware Size: 102.16 KB Download (28): Proteomic Mass Spectrometer Interface Download

Added: September 16, 2013 | Visits: 239

Fragmentation Analyzer Fragmentation Analyzer is a tool for analyzing MS/MS fragmentation data. Currently nine different analysis types are supported: * Spectra Visualization - visualize the MS/MS spectra with fragment ion annotation, zooming and manual de-novo-sequencing. * Intensity Box Plots - analyze intensity... Platforms: Mac

License: Freeware Size: 15.27 MB Download (16): Fragmentation Analyzer Download

Added: June 28, 2013 | Visits: 348

dnaTools Xplorer dnaLIMS is a state-of-the art web based laboratory information management system used to track and manage core facility workflow in high throughput environments. Its database and process flow can be customized to your core facility requirements. dnaLIMS process flow is used to capture DNA... Platforms: Mac

License: Freeware Size: 3.16 MB Download (16): dnaTools Xplorer Download

Added: November 14, 2013 | Visits: 181

Peptizer Manual validation of MS/MS driven peptide identification is a critical evaluation process relying on expert knowledge. Following the onset of large-scale proteomic endeavors, manual validation has become a undoable endeavor useful expert knowledge remains unused. The Peptizer platform was... Platforms: Mac

License: Freeware Size: 30.62 MB Download (17): Peptizer Download

Added: November 29, 2013 | Visits: 210

OMSSA Parser The Open Mass Spectrometry Search Algorithm [OMSSA] is an efficient search engine for identifying MS/MS peptide spectra by searching libraries of known protein sequences. OMSSA scores significant hits with a probability score developed using classical hypothesis testing, the same statistical... Platforms: Mac

License: Freeware Size: 22.1 MB Download (19): OMSSA Parser Download

Added: November 10, 2013 | Visits: 305

XTandem Parser X! Tandem open source is software that can match tandem mass spectra with peptide sequences, in a process that has come to be known as protein identification. This software has a very simple, sophisticated application programming interface (API): it simply takes an XML file of instructions on... Platforms: Mac

License: Freeware Size: 2.97 MB Download (20): XTandem Parser Download

Added: June 08, 2013 | Visits: 188

nebseq nebseq is a Python module for basic biological sequence manipulations. Import as usual >>> import nebseq Reverse complements The only note here is that revcomp does not check the input sequence to see if it looks like DNA or RNA. >>> nebseq.revcomp('ACGT') 'ACGT' >>>... Platforms: *nix

License: Freeware Size: 10.24 KB Download (18): nebseq Download