Algorithms for mapping short degenerate and weighted sequences to a reference genome

Pavlos Antoniou, S. Costas Iliopoulos, Laurent Mouchard, P. Solon Pissis

Research output: Contribution to JournalArticleAcademicpeer-review


Novel high-throughput (Deep) sequencing technologies have redefined the way genome sequencing is performed. They are able to produce millions of short sequences in a single experiment and with a much lower cost than previous methods. In this paper, we address the problem of efficiently mapping and classifying millions of short sequences to a reference genome, based on whether they occur exactly once in the genome or not, and by taking into consideration probability scores. In particular, we design algorithms for Massive Exact and Approximate Pattern Matching of short degenerate and weighted sequences, derived from Deep sequencing technologies, to a reference genome.

Original languageEnglish
Pages (from-to)385-397
Number of pages13
JournalInternational Journal of Computational Biology and Drug Design
Issue number4
Publication statusPublished - 1 Jan 2009
Externally publishedYes


  • Deep sequencing
  • Degenerate sequences
  • High-throughput sequencing
  • String algorithms
  • Weighted sequences


Dive into the research topics of 'Algorithms for mapping short degenerate and weighted sequences to a reference genome'. Together they form a unique fingerprint.

Cite this