myProMS 3.9.3 – Management, Validation and Interpretation of MS-based Proteomic data

myProMS 3.9.3

:: DESCRIPTION

myProMS is a comprehensive bioinformatics environment (database and web server) for management of Mass Spectrometry (MS) protein identification data generated by database-search engines such as Mascot or Sequest. Multiple functionalities are available to mine, validate and interpret the data from both MS and biological point of views. In particular, biological interpretation of the results is facilitated through the use of sophisticated data comparison modules, annotation enrichments and links to external resources. myProMS was designed to optimize data access and sharing during collaboration between users with complementary expertises; typically MS experts and biologists.

::DEVELOPER

Institut Curie, Bioinformatics Core Facility

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/MacOsx
Apache
Perl
MySQL
R package

:: DOWNLOAD

myProMS

:: MORE INFORMATION

Citation

Poullet P, Carpentier S, Barillot E.
myProMS, a web server for management and validation of mass spectrometry-based proteomic data.
Proteomics. 2007, 7 (15):2553-6.

VTAM 0.1.21 – Validation and Taxonomic Assignation of Metabarcoding Data

VTAM 0.1.21

:: DESCRIPTION

VTAM is a metabarcoding pipeline. The analyses start from high throughput sequencing (HTS) data of amplicons of one or several metabarcoding markers and produce an Amplicon Sequence Variant (ASV or variant) table of validated variants assigned to taxonomic groups.

::DEVELOPER

The TAGC Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

VTAM

:: MORE INFORMATION

Citation:

González, A., Dubut, V., Corse, E., Mekdad, R., Dechatre, T. and Meglécz, E..
VTAM: A robust pipeline for processing metabarcoding data using internal controls.
bioRxiv: 10.1101/2020.11.06.371187v1.

Peptizer 1.8.4 – Automating manual Validation of MS/MS Search results

Peptizer 1.8.4

:: DESCRIPTION

The Peptizer platform was created to automate the manual validation process by an expert system. The user can create a rule set via by enabling a set of Agent objects that will each inspect an assumption based on expert knowledge. Subsequent aggregation of multiple Agent inspection the enables separation of peptide identifications by these rules.

::DEVELOPER

Computational Omics and Systems Biology Group

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / MacOsX
Java

:: DOWNLOAD

Peptizer

:: MORE INFORMATION

Citation

Helsens et al.
Peptizer: A tool for assessing false positive peptide identifications and manually validating selected results.
Molecular & cellular proteomics : MCP (2008) vol. 7 (12) pp. 2363-72.

ProTSAV 1.0 – Protein Tertiary Structure Analysis and Validation server

ProTSAV 1.0

:: DESCRIPTION

ProTSAV is a meta-server, which has a collection of model quality assessment programs that evaluate the quality of a protein and correctness of the structural model.

::DEVELOPER

Supercomputing Facility for Bioinformatics & Computational Biology, IIT Delhi

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

ProTSAV

:: MORE INFORMATION

Citation:

ProTSAV: A protein tertiary structure analysis and validation server.
Singh A, Kaushik R, Mishra A, Shanker A, Jayaram B.
Biochim Biophys Acta. 2015 Oct 15. pii: S1570-9639(15)00260-5. doi: 10.1016/j.bbapap.2015.10.004.

ValWorkBench 1.0 – Java library for Cluster Validation

ValWorkBench 1.0

:: DESCRIPTION

ValWorkBench consists of a collection of measures for validation of clustering solutions and algorithms. It has external measures, as the Adjusted Rand index, and internal measures as Figure of Merit, Gap Statistics, Within Cluster Sum Square, Consensus Clustering and more.

::DEVELOPER

Raffaele Giancarlo

:: SCREENSHOTS

:: REQUIREMENTS

Linux / MacOSX / Windows
Java

:: DOWNLOAD

ValWorkBench

:: MORE INFORMATION

Citation

ValWorkBench: an open source Java library for cluster validation, with applications to microarray data analysis.
Giancarlo R, Scaturro D, Utro F.
Comput Methods Programs Biomed. 2015 Feb;118(2):207-17. doi: 10.1016/j.cmpb.2014.12.004.

Twilight 1.13 – A tool for Ligand Density Validation

Twilight 1.13

:: DESCRIPTION

Twilight is a standalone script for analysis, visualization, and annotation of a pre-filtered set of protein/ligand complexes deposited with the PDB with ligand RSCC values that are below a threshold of 0.6.

::DEVELOPER

Twilight team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ Windows/ MacOsX
Python

:: DOWNLOAD

Twilight

:: MORE INFORMATION

Citation:

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013 Feb 1;69(Pt 2):195-200. doi: 10.1107/S1744309112044387.
Visualizing ligand molecules in Twilight electron density.
Weichenberger CX1, Pozharski E, Rupp B.

SATIVA 0.9 – Semi-Automatic Taxonomy Improvement and Validation Algorithm

SATIVA 0.9

:: DESCRIPTION

SATIVA is a pipeline that uses Evolutionary Placement Algorithm (EPA) to identify taxonomically mislabeled sequences and suggest corrections.

::DEVELOPER

Alexey Kozlov

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX
Python

:: DOWNLOAD

SATIVA

:: MORE INFORMATION

Citation

Phylogeny-aware identification and correction of taxonomically mislabeled sequences.
Kozlov AM, Zhang J, Yilmaz P, Glöckner FO, Stamatakis A.
Nucleic Acids Res. 2016 May 10. pii: gkw396

WOOF – Word-oriented Objective Function for Validation of Sequence Alignments

WOOF

:: DESCRIPTION

WOOF (Word-oriented objective function) is a method designed to rigourously apply the principle of visual alignment validation. WOOF does not actually make changes to a multiple sequence alignment, but is intead intended to choose the best alignment of a set of proteins from a set of such alignments that have been generated using different algorithms and parameter settings. The winning alignment is the one that best aligns a set of conserved patterns extracted using a pattern-finding approach such as TEIRESIAS. Patterns are weighted based on their statistical significance and position relative to other patterns.

::DEVELOPER

Beiko lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Mac OsX / Linux
Perl

:: DOWNLOAD

WOOF

:: MORE INFORMATION

Citation

Beiko, R.G., Chan, C.X., and Ragan, M.A. (2005)
A word-oriented approach to alignment validation
Bioinformatics 21: 2230-2239

PSVS 1.5 – Protein Structure Validation Software Suite

PSVS 1.5

:: DESCRIPTION

PSVS systematically evaluates the quality of protein structures. PSVS integrates analyses from several widely-used structure quality evaluation tools, including RPF , PROCHECK, MolProbity , Verify3D Prosa II , the PDB validation software, and various structure-validation tools.PSVS provides standard constraint analyses, statistics on the PDB validation goodness-of-fit between structures and experimental data, and knowledge-based structure quality scores in standardized format suitable for database integration. Global quality measures are reported as Z scores, based on calibration with a set of high-resolution X-ray crystal structures.

::DEVELOPER

CABM Structural Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web BRowser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Proteins. 2007 Mar 1;66(4):778-95.
Evaluating protein structures determined by structural genomics consortia.
Bhattacharya A, Tejero R, Montelione GT.

TAP 1.1 – Protein Structure Validation

TAP 1.1

:: DESCRIPTION

TAP serves to validate the local torsion angles of a protein structure. The server computes both an overall conformational score of a protein structure and a confidence estimate.

::DEVELOPER

The BioComputing UP lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

TAP

:: MORE INFORMATION

Citation:

Silvio C.E. Tosatto and Roberto Battistutta.
TAP score: torsion angle propensity normalization applied to local protein structure evaluation.
BMC Bioinformatics, accepted for publication. (2007)