The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing

Bioinformatics. 2010 Jan 1;26(1):38-45. doi: 10.1093/bioinformatics/btp614. Epub 2009 Oct 27.


Motivation: The advent of next-generation sequencing technologies has increased the accuracy and quantity of sequence data, opening the door to greater opportunities in genomic research.

Results: In this article, we present GNUMAP (Genomic Next-generation Universal MAPper), a program capable of overcoming two major obstacles in the mapping of reads from next-generation sequencing runs. First, we have created an algorithm that probabilistically maps reads to repeat regions in the genome on a quantitative basis. Second, we have developed a probabilistic Needleman-Wunsch algorithm which utilizes _prb.txt and _int.txt files produced in the Solexa/Illumina pipeline to improve the mapping accuracy for lower quality reads and increase the amount of usable data produced in a given experiment.

Availability: The source code for the software can be downloaded from

MeSH terms

  • Algorithms*
  • Base Sequence
  • Chromosome Mapping / methods*
  • DNA / genetics*
  • Data Interpretation, Statistical
  • Molecular Sequence Data
  • Sequence Analysis, DNA / methods*
  • Software*


  • DNA