MAPS specifications


Unique identifier OMICS_33156
Alternative name mRNA Assembler for ProteogenomicS
Software type Application/Script
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data Some aligned reads from unsorted SAMs or BAMs.
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes




No version available


  • person_outline Maxim Shokhirev

Publication for mRNA Assembler for ProteogenomicS

MAPS citation


The influence of transcript assembly on the proteogenomics discovery of microproteins

PLoS One
PMCID: 5870951
PMID: 29584760
DOI: 10.1371/journal.pone.0194518

[…] . All parameters must be manually optimized for each dataset to avoid biasing downstream searching, while maintaining accurate transcript reconstruction.Therefore, we developed a new assembler called mRNA Assembler for ProteogenomicS (MAPS) to explore the influence of these considerations on microprotein discovery (). From RNA-Seq mapped reads, MAPS assembles a collection of open reading frames wi […]

MAPS institution(s)
Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA; Razavi Newman Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, CA, USA
MAPS funding source(s)
Supported by the Razavi Newman Integrative Genomics and Bioinformatics Core and Next Generation Sequencing Core Facilities of the Salk Institute with funding from NIH-NCICCSG:P30 014195, the Chapman Foundation and the Helmsley Charitable Trust; by Larry Hillblom Foundation Fellowship Grant; by NIH (R01 GM102491), the NCI Cancer Center Support Grant P30 (CA014195 MASS core), The Leona M. and Harry B. Helmsley Charitable Trust grant (#2012-PG-MED002), and Dr. Frederick Paulsen Chair/Ferring Pharmaceuticals.

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