Tag: proteomic

Genoppi 1.0.13 – Integration of Proteomic and Genetic data

Genoppi 1.0.13

:: DESCRIPTION

Genoppi is an open-source software for performing quality control and analyzing quantitative proteomic data. Genoppi streamlines the integration of proteomic data with external datasets such as known protein-protein interactions in published literature, data from genetic studies, gene set annotations, or other user-defined inputs.

::DEVELOPER

Lage Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

Genoppi

:: MORE INFORMATION

Citation

Pintacuda G, Lassen FH, Hsu YH, Kim A, Martín JM, Malolepsza E, Lim JK, Fornelos N, Eggan KC, Lage K.
Genoppi is an open-source software for robust and standardized integration of proteomic and genetic data.
Nat Commun. 2021 May 10;12(1):2580. doi: 10.1038/s41467-021-22648-5. PMID: 33972534; PMCID: PMC8110583.

GOfact 20051017 – An Integrated Strategy for Functional Analysis in Large-scale Proteomic Research by Gene Ontology

GOfact 20051017

:: DESCRIPTION

GOfact is developed to identify the functional distribution and the significantly enriched functional categories of the proteomic expression profile. It would be helpful for understanding the overall functions of these identified proteins and supply the fundamental information for further bioinformatics exploration.

::DEVELOPER

Li Dong

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows
  • Perl

:: DOWNLOAD

  GOfact

:: MORE INFORMATION

Citation

Li Dong, Li Jian-Qi, Ouyang Shu-Guang, Wang Jian, Xu Xiaojie, Zhu Yun-Ping, He Fu-Chu.
An Integrated Strategy for Functional Analysis in Large-scale Proteomic Research by Gene Ontology.
Biochemistry and Biophysics 2005,32(11):1026-1029

GPKB – Genomic and Proteomic Knowledge Base

GPKB

:: DESCRIPTION

GPKB integrates several of the most relevant sources of such dispersed information (including Entrez Gene, UniProt, IntAct, Expasy Enzyme, GO, GOA, BioCyc, KEGG, Reactome, and OMIM).

::DEVELOPER

GPKB team

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Masseroli M, Canakoglu A, Ceri S.
Integration and Querying of Genomic and Proteomic Semantic Annotations for Biomedical Knowledge Extraction.
IEEE/ACM Trans Comput Biol Bioinform. 2016 Mar-Apr;13(2):209-19. doi: 10.1109/TCBB.2015.2453944. PMID: 27045824.

MassSpec 1.1 – Peak list Extraction from Proteomic Mass Spectra

MassSpec 1.1

:: DESCRIPTION

MassSpecis a MATLAB implementation of the peak list extraction procedure

::DEVELOPER

laboratorio di Bioinformatica e Biologia Sintetica – Univ. of Pavia

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • Matlab

:: DOWNLOAD

 MassSpec

:: MORE INFORMATION

Citation

BMC Bioinformatics 2010, 11:518 doi:10.1186/1471-2105-11-518
Accurate peak list extraction from proteomic mass spectra for identification and profiling studies.
Barbarini N, Magni P.

Dintor – Functional Annotation of Genomic and Proteomic data

Dintor

:: DESCRIPTION

Dintor is a data integration framework that provides a set of over 30 tools to assist researchers in the exploration of genomics and proteomics datasets.

::DEVELOPER

the Center of Biomedicine (CBM)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Dintor

:: MORE INFORMATION

Citation

Dintor: functional annotation of genomic and proteomic data.
Weichenberger CX, Blankenburg H, Palermo A, D’Elia Y, K?nig E, Bernstein E, Domingues FS.
BMC Genomics. 2015 Dec 21;16(1):1081. doi: 10.1186/s12864-015-2279-5.

BISQUE 1.0 – a human Genomic, Proteomic, and Transcriptomic Conversion tool

BISQUE 1.0

:: DESCRIPTION

BISQUE (The Biological Sequence Exchange) is a bioinformatics tool enabling locus and variant-specific conversion among human gene, transcript, and protein identifiers from several popular databases.

::DEVELOPER

Yu Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

  BISQUE

:: MORE INFORMATION

Citation

BISQUE: locus- and variant-specific conversion of genomic, transcriptomic, and proteomic database identifiers.
Meyer MJ, Geske P, Yu H.
Bioinformatics. 2016 Jan 23. pii: btw043.

Peppy – Proteogenomic, Proteomic search tool

Peppy

:: DESCRIPTION

Peppy: a fully integrated, proteogenomic mapping software tool. Peppy generates a peptide database from genome files, tracks peptide loci, matches peptides to MS/MS spectra, assigns scores to those matches, and tracks score distributions to find E-Values. To determine false discovery rate thresholds, Peppy automatically generates a decoy database from the original genome files and repeats the entire search process.

::DEVELOPER

The Giddings Lab at Boise State

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

 Peppy

:: MORE INFORMATION

Citation

Peppy: proteogenomic search software.
Risk BA, Spitzer WJ, Giddings MC.
J Proteome Res. 2013 Jun 7;12(6):3019-25. doi: 10.1021/pr400208w.

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