Dataset Information

MSMSpdbb: providing protein databases of closely related organisms to improve proteomic characterization of prokaryotic microbes.

ABSTRACT: UNLABELLED: The Microbial Proteomic Resource (MPR) is a repository service that contains non-redundant protein databases of related bacterial strains, which were generated through an in-house developed software called Multi-Strain Mass Spectrometry Prokaryotic DataBase Builder (MSMSpdbb). MSMSpdbb merges and clusters protein sequences inferred from genomic sequences, and provide a protein list in FASTA format that covers for divergence in gene annotation, translational start site choice and presence of single nucleotide polymorphisms and other mutations. AVAILABILITY: MSMSpdbb was developed in C++ using the Qt libraries (Nokia) and licensed under the GNU General Public License version 2. MSMSpdbb is freely available, and its installation files, instructions for use and additional documentation can be found at the MPR web site http://org.uib.no/prokaryotedb/ can also be found at Proteomecommons.org (see Supplementary Methods for Hash number).

SUBMITTER: de Souza GA

PROVIDER: S-EPMC2828113 | biostudies-literature | 2010 Mar

REPOSITORIES: biostudies-literature

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MSMSpdbb: providing protein databases of closely related organisms to improve proteomic characterization of prokaryotic microbes.

de Souza Gustavo A GA Arntzen Magnus Ø MØ Wiker Harald G HG

Bioinformatics (Oxford, England) 20100114 5

<h4>Unlabelled</h4>The Microbial Proteomic Resource (MPR) is a repository service that contains non-redundant protein databases of related bacterial strains, which were generated through an in-house developed software called Multi-Strain Mass Spectrometry Prokaryotic DataBase Builder (MSMSpdbb). MSMSpdbb merges and clusters protein sequences inferred from genomic sequences, and provide a protein list in FASTA format that covers for divergence in gene annotation, translational start site choice a ...[more]

PMID: 20080508

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Project description:BackgroundThe procedural aspects of genome sequencing and assembly have become relatively inexpensive, yet the full, accurate structural annotation of these genomes remains a challenge. Next-generation sequencing transcriptomics (RNA-Seq), global microarrays, and tandem mass spectrometry (MS/MS)-based proteomics have demonstrated immense value to genome curators as individual sources of information, however, integrating these data types to validate and improve structural annotation remains a major challenge. Current visual and statistical analytic tools are focused on a single data type, or existing software tools are retrofitted to analyze new data forms. We present Visual Exploration and Statistics to Promote Annotation (VESPA) is a new interactive visual analysis software tool focused on assisting scientists with the annotation of prokaryotic genomes though the integration of proteomics and transcriptomics data with current genome location coordinates.ResultsVESPA is a desktop Java™ application that integrates high-throughput proteomics data (peptide-centric) and transcriptomics (probe or RNA-Seq) data into a genomic context, all of which can be visualized at three levels of genomic resolution. Data is interrogated via searches linked to the genome visualizations to find regions with high likelihood of mis-annotation. Search results are linked to exports for further validation outside of VESPA or potential coding-regions can be analyzed concurrently with the software through interaction with BLAST. VESPA is demonstrated on two use cases (Yersinia pestis Pestoides F and Synechococcus sp. PCC 7002) to demonstrate the rapid manner in which mis-annotations can be found and explored in VESPA using either proteomics data alone, or in combination with transcriptomic data.ConclusionsVESPA is an interactive visual analytics tool that integrates high-throughput data into a genomic context to facilitate the discovery of structural mis-annotations in prokaryotic genomes. Data is evaluated via visual analysis across multiple levels of genomic resolution, linked searches and interaction with existing bioinformatics tools. We highlight the novel functionality of VESPA and core programming requirements for visualization of these large heterogeneous datasets for a client-side application. The software is freely available at https://www.biopilot.org/docs/Software/Vespa.php.

Dataset Information

MSMSpdbb: providing protein databases of closely related organisms to improve proteomic characterization of prokaryotic microbes.

Publications

MSMSpdbb: providing protein databases of closely related organisms to improve proteomic characterization of prokaryotic microbes.

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