Journal: Molecular & Cellular Proteomics : MCP

Article Title: Methods, Tools and Current Perspectives in Proteogenomics *

doi: 10.1074/mcp.MR117.000024

Figure Lengend Snippet: Software pipelines for generating personalized protein sequence databases

Article Snippet: Several informatics pipelines have emerged in recent years for generating these databases ( 59 – 66 ). illustrates the core processes these pipelines perform, and provides a list of typical, currently available software. table ft1 table-wrap mode="anchored" t5 caption a7 Name URL Reference Remarks customProDB https://www.bioconductor.org/packages/release/bioc/html/customProDB.html ( 63 ) R-package to generate customized protein database from NGS data, including SNVs, INDELs and novel splice junctions Galaxy Integrated Omics https://bessantlab.org/software/gio/ ( 60 ) Curated collection of Galaxy-based tools to generate sample-specific databases from RNA-seq data Galaxy-P https://toolshed.g2.bx.psu.edu/view/galaxyp/proteomics_rnaseq_sap_db_workflow/3a11830963e3 ( 201 ) Collection of Galaxy-P workflows for customized database construction from RNA-seq data QUILTS http://quilts.fenyolab.org ( 62 ) Web-based tool to generate sample-specific databases with special focus on novel splice isoforms MutationDB http://proteomics.ucsd.edu/software-tools/cancer-proteogenomics-4/ ( 65 ) Proteogenomic database construction from all types of mutational variants driven from large-scale RNA-seq data SpliceDB http://proteomics.ucsd.edu/software-tools/cancer-proteogenomics-4/ ( 65 ) Proteogenomic database construction with special focus on novel splice junction identifications driven from large-scale RNA-seq data PGA http://bioconductor.org/packages/PGA/ ( 64 ) R-package to build customized protein databases based on RNA-Seq data with or without a reference genome guide JUMPg https://github.com/gatechatl/JUMPg ( 61 ) Perl-based pipeline to build search customized databases and to perform subsequent filtering and visualization of search results MSProGene http://sourceforge.net/projects/msprogene/ ( 66 ) Java program that constructs customized protein databases from RNA-seq data PPLine https://sourceforge.net/projects/ppline/ ( 202 ) Python-based suite to process raw RNA-seq or Exome-seq data for customized database construction Open in a separate window caption a8 Software pipelines for generating personalized protein sequence databases Because the likelihood of experimentally observing a peptide decreases as one progresses from a reference database to each variant database (SAAV; novel splice junctions; and novel coding loci in putative intergenic regions), MS/MS data sets are sensibly searched in an iterative fashion through individual databases with separate FDR estimations for PSMs ( 12 , 13 , 62 , 67 ).

Techniques: Software, Sequencing, Construct