title: MR-Tandem: parallel X!Tandem using Hadoop MapReduce on Amazon Web Services.
abstract: CONCLUSIONS
  MR-Tandem adapts the popular X!Tandem peptide search engine to work with Hadoop MapReduce for reliable parallel execution of large searches. MR-Tandem runs on any Hadoop cluster but offers special support for Amazon Web Services for creating inexpensive on-demand Hadoop clusters, enabling search volumes that might not otherwise be feasible with the compute resources a researcher has at hand. MR-Tandem is designed to drop in wherever X!Tandem is already in use and requires no modification to existing X!Tandem parameter files, and only minimal modification to X!Tandem-based workflows.
  
  
  METHODS
  MR-Tandem is implemented as a lightly modified X!Tandem C++ executable and a Python script that drives Hadoop clusters including Amazon Web Services (AWS) Elastic Map Reduce (EMR), using the modified X!Tandem program as a Hadoop Streaming mapper and reducer. The modified X!Tandem C++ source code is Artistic licensed, supports pluggable scoring, and is available as part of the Sashimi project at http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/trans_proteomic_pipeline/extern/xtandem/. The MR-Tandem Python script is Apache licensed and available as part of the Insilicos Cloud Army project at http://ica.svn.sourceforge.net/viewvc/ica/trunk/mr-tandem/. Full documentation and a windows installer that configures MR-Tandem, Python and all necessary packages are available at this same URL.
  
  
  BACKGROUND
  brian.pratt@insilicos.com
authors.affiliation: Insilicos LLC, Seattle WA, USA.
authors.forename: Brian
authors.initials: B
authors.lastname: Pratt
authors.forename: J Jeffry
authors.initials: JJ
authors.lastname: Howbert
authors.forename: Natalie I
authors.initials: NI
authors.lastname: Tasman
authors.forename: Erik J
authors.initials: EJ
authors.lastname: Nilsson
mesh_terms: D016000:Cluster Analysis; D011381:Programming Languages; D011499:Protein Processing, Post-Translational; D011506:Proteins / Q000032:analysis* / Q000378:metabolism*; D057386:Search Engine; D012984:Software / Q000191:economics
chemical_list: D011506:Proteins
references.citation: Bioinformatics. 2004 Jun 12;20(9):1466-7
references.pmid: 14976030
references.citation: J Proteome Res. 2005 Sep-Oct;4(5):1842-7
references.pmid: 16212440
references.citation: J Proteome Res. 2008 Jan;7(1):293-9
references.pmid: 17902638