HomologMiner

HomologMiner is a software tool designed to identify and cluster homologous DNA sequences at the whole genome level, excluding low-complexity repeats, tandem repeats, and annotated interspersed repeats. The program determines the boundaries of each group member so that it closely represents a biological unit, such as a complete gene or a partial gene coding a protein domain. The software tool, HomologMiner, was applied to the whole genomes of human, macaque, and mouse, and the obtained groups include gene families, unannotated interspersed repeats, and additional homologous groups resulting from recent segmental duplications.

Topic

Genetics;Sequence homology analysis

Detail

  • Operation: Sequence similarity analysis; Sequence clustering; Sequence alignment

  • Software interface: Command-line user inteface

  • Language: C++

  • License: Not stated

  • Cost: Free

  • Version name: 1.00

  • Credit: -

  • Input: blastz-output-file

  • Output: .nodes (boundaries of each region), .edges (graph formed by duplicate units), .cccs (homologous groups), .dup (tags of duplications), .rep (tags of excessive repeats).

  • Contact: mhou@cse.psu.edu

  • Collection: -

  • Maturity: Stable

Publications

  • HomologMiner: looking for homologous genomic groups in whole genomes.
  • Hou M, et al. HomologMiner: looking for homologous genomic groups in whole genomes. HomologMiner: looking for homologous genomic groups in whole genomes. 2007; 23:917-25. doi: 10.1093/bioinformatics/btm048
  • https://doi.org/10.1093/bioinformatics/btm048
  • PMID: 17308341
  • PMC: -

Download and documentation

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