MixGF 1.0r – Computing Statistical Significance of Peptide-spectrum-matches for multiplexed MS/MS Spectra

MixGF 1.0r

:: DESCRIPTION

MixGF computes the statistical significance of peptide identifications for mixture spectra and show that this approach improves the sensitivity of current mixture spectra database search tools by a ≈30-390%.

::DEVELOPER

CCMS The Center for Computational Mass Spectrometry

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 MixGF

:: MORE INFORMATION

Citation

Mol Cell Proteomics. 2014 Dec;13(12):3688-97. doi: 10.1074/mcp.O113.037218. Epub 2014 Sep 15.
MixGF: Spectral Probabilities for Mixture Spectra from more than One Peptide.
Wang J, Bourne PE, Bandeira N

GAS2 20061018 – Evaluating Statistical Significance in Two-Stage Genomewide Association Studies

GAS2 20061018

:: DESCRIPTION

GAS2 provides a FORTRAN-77 program to evaluate statistical significance in two-stage genomewide association studies.

::DEVELOPER

Danyu Lin

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • FORTRAN-77

:: DOWNLOAD

 GAS2

:: MORE INFORMATION

Citation

Lin (2006),
Evaluating statistical significance in two-stage genomewide association studies“,
American Journal of Human Genetics, 78(3):505-509.

GLOBAL 1.0 – Statistical Significance of Semi-global Block Alignments

GLOBAL 1.0

:: DESCRIPTION

GLOBAL (GLObal Blocks Aligned Locally) gives the statistical significance of semi-global block alignments.

::DEVELOPER

Statistical Computational Biology Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows / MacOsX

:: DOWNLOAD

 GLOBAL

:: MORE INFORMATION

Citation

M.G. Kann, S.L. Sheetlin, Y. Park, S.H. Bryant, and J.L. Spouge
The identification of complete domains within protein sequences using accurate E-values for semi- global alignment
(2007) Nucl Acids Res 35 : 4678-4685

PairwiseStatSig 20110801 – Pairwise Statistical Significance

PairwiseStatSig 20110801

:: DESCRIPTION

PairwiseStatSig estimates the pairwise statistical significance of a pairwise local alignment of two protein sequences independent of any database using censored Maximum Likelihood Fitting.

::DEVELOPER

The Brendel Group @ Indiana University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

PairwiseStatSig

:: MORE INFORMATION

Citation

Agrawal, A., Brendel, V. & Huang, X. (2008)
Pairwise statistical significance versus database statistical significance for local alignment of protein sequences.
BMC Bioinformatics 2009, 10(Suppl 3):S1

COMPASS 3.1 – COmparison of Multiple Protein Sequence Alignments with assessment of Statistical Significance.

COMPASS 3.1

:: DESCRIPTION

COMPASS runs a search with submitted alignment (or sequence) as a query against a database of protein families.

::DEVELOPER

Grishin Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 COMPASS

:: MORE INFORMATION

Citation:

R.I. Sadreyev, M. Tang, B. Kim and N.V. Grishin (2009)
COMPASS server for homology detection: improved statistical accuracy, speed, and functionality.
Nucleic Acids Res doi:10.1093/nar/gkp360.

GPASS 1.0 – Genome-wide Poisson Approximation for Statistical Significance

GPASS 1.0

:: DESCRIPTION

GPASS (Genome-wide Poisson Approximation for Statistical Significance) detects SNP disease associations in case control studies, controls FWER and FDR adjusting for dependence/linkage disequilibrium.

::DEVELOPER

Yu Zhang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GPASS

:: MORE INFORMATION