CombAlign: A protein sequence comparison algorithm considering recombinations

Katja Wegner, Stephan Jansen, Stefan Wuchty, Ralph Gauges, Ursula Kummer

Research output: Contribution to journalArticlepeer-review

2 Scopus citations


The basic linear treatment of sequence comparisons limits the ability of contemporary sequence alignment algorithms to detect non-order-conserving recombinations. Here, we introduce the algorithm combAlign which addresses the assessment of pairwise sequence similarity on non-order-conserving recombinations on a large scale. Emphasizing a two-level approach, combAlign first detects locally well conserved subsequences in a target and a source sequence. Subsequently, the relative placement of alignments is mapped to a graph. Concatenating local alignments to reassemble the target sequence to the fullest extent, the maximum scoring path through the graph denotes the best attainable combAlignment. Parameters influencing this process can be set to meet the user's specific demands. combAlign is applied to examples demonstrating the possibility to reflect evolutionary kinship of proteins even if their domains and motifs are strongly rearranged.

Original languageEnglish (US)
Pages (from-to)243-254
Number of pages12
JournalIn Silico Biology
Issue number3
StatePublished - Dec 17 2004
Externally publishedYes


  • DAG
  • Dynamic programming
  • Graph theory
  • Point mutations
  • Shuffling events

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Computational Mathematics
  • Computational Theory and Mathematics


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