MMuFLR: missense mutation and frameshift location reporter

• DOI: 10.1093/bioinformatics/btt385
• Publication Date: 2013-07-04T07:00:34Z
• Authors: Susan K. Rathe; James E. Johnson; Kevin A.T. Silver...; Jesse J. Erdmann; Adrienne L. Watson; Flavia E. Popescu; John R. Ohlfest; David A. Largaespada
• Keywords: 0301 basic medicine; 03 medical and health sciences; Sequence Analysis, RNA; Mutation, Missense; High-Throughput Nucleotide Sequencing; Humans; Frameshift Mutation; Software; Neoplasm Proteins; 3. Good health

Abstract Motivation: Cancer researchers seeking immunotherapy targets in cancer cells need tools to locate highly expressed proteins unique cells. Missense mutation and frameshift location reporter (MMuFLR), a Galaxy-based workflow, analyzes next-generation sequencing paired read RNA-seq output reliably identify small mutations missense protein-coding genes. MMuFLR ignores known SNPs, low quality reads poly-A/T sequences. For each identified, provides the sequence of amino acid substitutions novel protein candidates for direct input into epitope evaluation tools. Availability: http://toolshed.g2.bx.psu.edu/ Contact: [e-mail] or [e-mail] Supplementary information: data are available at Bioinformatics online.