Tag: Peptide

sapFinder 1.26.0 – Detection of Variant Peptides in Shotgun Proteomics Experiments

sapFinder 1.26.0

:: DESCRIPTION

sapFinder is developed to automate (1) variation-associated database construction, (2) database searching, (3) post-processing, (4) HTML-based report generation in shotgun proteomics.

::DEVELOPER

 Shaohang Xu <xsh.skye at gmail.com>, Bo Wen <wenbo at genomics.cn>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • R
  • BioCOnductor

:: DOWNLOAD

 sapFinder

:: MORE INFORMATION

Citation

sapFinder: an R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments.
Wen B, Xu S, Sheynkman GM, Feng Q, Lin L, Wang Q, Xu X, Wang J, Liu S.
Bioinformatics. 2014 Jul 22. pii: btu397.

iSuc-PseAAC – Predicting Lysine Succinylation in proteins by incorporating Peptide Position-specific Propensity

iSuc-PseAAC

:: DESCRIPTION

The web-server iSuc-PseAAC is established for predicting the lysine succinylation sites in proteins.

::DEVELOPER

Yan Xu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

iSuc-PseAAC: predicting lysine succinylation in proteins by incorporating peptide position-specific propensity.
Xu Y, Ding YX, Ding J, Lei YH, Wu LY, Deng NY.
Sci Rep. 2015 Jun 18;5:10184. doi: 10.1038/srep10184.

sapFinder 1.20.1 – Variant Peptides Detection and Visualization in Shotgun Proteomics.

sapFinder 1.20.1

:: DESCRIPTION

sapFinder is developed to automate (1) variation-associated database construction, (2) database searching, (3) post-processing, (4) HTML-based report generation in shotgun proteomics.

::DEVELOPER

Shaohang Xu <xsh.skye at gmail.com>, Bo Wen <wenbo at genomics.cn>

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux /Windows / MacOs
  • R
  • BioConductor

:: DOWNLOAD

 sapFinder

:: MORE INFORMATION

Citation

sapFinder: an R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments.
Wen B, Xu S, Sheynkman GM, Feng Q, Lin L, Wang Q, Xu X, Wang J, Liu S.
Bioinformatics. 2014 Nov 1;30(21):3136-8. doi: 10.1093/bioinformatics/btu397.

specL 1.26.0 – Prepare Peptide Spectrum Matches for Use in Targeted Proteomics

specL 1.26.0

:: DESCRIPTION

specL provides a function for generating spectra libraries which can be used for MRM SRM MS workflows in proteomics. The package provides a BiblioSpec reader, a function which can add the protein information using a FASTA formatted amino acid file, and an export method for using the created library in the Spectronaut software.

::DEVELOPER

specL team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux /MacOsX
  • R/Bioconductor

:: DOWNLOAD

 specL

:: MORE INFORMATION

Citation:

specL – An R/Bioconductor package to prepare peptide spectrum matches for use in targeted proteomics.
Panse C, Trachsel C, Grossmann J, Schlapbach R.
Bioinformatics. 2015 Feb 23. pii: btv105.

ProMatch – Match Peptide and mRNA Sequences to Entries in NCBI RefSeq

ProMatch

:: DESCRIPTION

ProMatch is a Java-based standalone program to match input parameters such as peptide and mRNA sequences to entries in NCBI Reference Sequence Database (RefSeq). ProMatch helps identify and eliminate ambiguous identifications from proteomic and transcriptomic data.

::DEVELOPER

Epithelial Systems Biology Laboratory

:: SCREENSHOTS

ProMatch

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • JRE

:: DOWNLOAD

ProMatch

:: MORE INFORMATION

Citation

Physiol Genomics. 2010 Feb 4;40(3):167-83. doi: 10.1152/physiolgenomics.00148.2009. Epub 2009 Dec 8.
Proteomic profiling of nuclei from native renal inner medullary collecting duct cells using LC-MS/MS.
Tchapyjnikov D1, Li Y, Pisitkun T, Hoffert JD, Yu MJ, Knepper MA.

AbDesigner – Design of Peptide-directed Antibodies

AbDesigner

:: DESCRIPTION

AbDesigner is a tool for analyzing the amino acid sequence of a given protein to identify optimal immunizing peptides for production of antibodies.

::DEVELOPER

Epithelial Systems Biology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WEb browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

NHLBI-AbDesigner: an online tool for design of peptide-directed antibodies.
Pisitkun T, Hoffert JD, Saeed F, Knepper MA.
Am J Physiol Cell Physiol. 2012 Jan 1;302(1):C154-64. doi: 10.1152/ajpcell.00325.2011.

UPF 0.912 – Unique Peptide Finder

UPF 0.912

:: DESCRIPTION

UPF is used to calculate sets of unique peptides from protein sequences. Furthermore, UPF provides the possibility to calculate both the frequency of peptides and to retrieve information from which proteins a particular peptide can be derived.

::DEVELOPER

Medizinisches Proteom-Center, Medical Bioinformatics

:: SCREENSHOTS

upf

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • JRE

:: DOWNLOAD

 UPF

:: MORE INFORMATION

Hammock v1.2.0 – Hidden Markov Model-based Peptide Clustering algorithm

Hammock v1.2.0

:: DESCRIPTION

Hammock is a tool for peptide sequence clustering. It is able to cluster extremely large amounts of short peptide sequences into groups sharing sequence motifs.

::DEVELOPER

REGIONAL CENTRE FOR APPLIED MOLECULAR ONCOLOGY (RECAMO)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Java
  • Clustal Omega
  • Hmmer3
  • HHsuite

:: DOWNLOAD

 Hammock

:: MORE INFORMATION

Citation:

Hammock: A Hidden Markov model-based peptide clustering algorithm to identify protein-interaction consensus motifs in large datasets.
Krejci A, Hupp T, Lexa M, Vojtesek B, Muller P.
Bioinformatics. 2015 Sep 5. pii: btv522

DCF 0.6 – Peptide Design by Compatible Functions

DCF 0.6

:: DESCRIPTION

DCF (Design by Compatible Functions) is a peptide design principle for multifunctional peptides based on similarity to a functional reference class.

::DEVELOPER

Christian Diener

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 DCF

:: MORE INFORMATION

Citation

Effective Design of Multifunctional Peptides by Combining Compatible Functions.
Diener C, Garza Ramos Martínez G, Moreno Blas D, Castillo González DA, Corzo G, Castro-Obregon S, Del Rio G.
PLoS Comput Biol. 2016 Apr 20;12(4):e1004786. doi: 10.1371/journal.pcbi.1004786.

PeakLink 1.0 – Peptide Peak Linking method in LC-MS/MS using Wavelet and SVM

PeakLink 1.0

:: DESCRIPTION

PeakLink (PL) uses information in both the time and frequency domain as inputs to a non-linear support vector machine (SVM) classifier. The PL algorithm first uses a threshold on retention time to remove candidate corresponding peaks with excessively large elution time shifts, then PL calculates the correlation between a pair of candidate peaks after removing noise through wavelet transformation. After converting retention time and peak shape correlation to statistical scores, an SVM classifier is trained and applied for differentiating corresponding and non-corresponding peptide peaks.

::DEVELOPER

PeakLink team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / Windows / MacOsX
  • MatLab

:: DOWNLOAD

 PeakLink

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Sep 1;30(17):2464-70. doi: 10.1093/bioinformatics/btu299. Epub 2014 May 9.
PeakLink: a new peptide peak linking method in LC-MS/MS using wavelet and SVM.
Ghanat Bari M, Ma X, Zhang J.