title: MMuFLR: missense mutation and frameshift location reporter.
abstract: BACKGROUND
  Cancer researchers seeking immunotherapy targets in cancer cells need tools to locate highly expressed proteins unique to cancer cells. Missense mutation and frameshift location reporter (MMuFLR), a Galaxy-based workflow, analyzes next-generation sequencing paired read RNA-seq output to reliably identify small frameshift mutations and missense mutations in highly expressed protein-coding genes. MMuFLR ignores known SNPs, low quality reads and poly-A/T sequences. For each frameshift and missense mutation identified, MMuFLR provides the location and sequence of the amino acid substitutions in the novel protein candidates for direct input into epitope evaluation tools.
  
  
  BACKGROUND
  http://toolshed.g2.bx.psu.edu/
  
  
  BACKGROUND
  rath0096@umn.edu or johns198@umn.edu
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA. rath0096@umn.edu
authors.forename: Susan K
authors.initials: SK
authors.lastname: Rathe
authors.forename: James E
authors.initials: JE
authors.lastname: Johnson
authors.forename: Kevin A T
authors.initials: KA
authors.lastname: Silverstein
authors.forename: Jesse J
authors.initials: JJ
authors.lastname: Erdmann
authors.forename: Adrienne L
authors.initials: AL
authors.lastname: Watson
authors.forename: Flavia E
authors.initials: FE
authors.lastname: Popescu
authors.forename: John R
authors.initials: JR
authors.lastname: Ohlfest
authors.forename: David A
authors.initials: DA
authors.lastname: Largaespada
mesh_terms: D016368:Frameshift Mutation; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D020125:Mutation, Missense; D009363:Neoplasm Proteins / Q000235:genetics; D017423:Sequence Analysis, RNA; D012984:Software
chemical_list: D009363:Neoplasm Proteins