MapToGenome: A comparative genomic tool that aligns transcript maps to sequenced genomes

Srikrishna Putta, Jeramiah J. Smith, Chuck Staben, S. Randal Voss

Research output: Contribution to journalArticlepeer-review

2 Scopus citations


Efforts to generate whole genome assemblies and dense genetic maps have provided a wealth of gene positional information for several vertebrate species. Comparing the relative location of orthologous genes among these genomes provides perspective on genome evolution and can aid in translating genetic information between distantly related organisms. However, large-scale comparisons between genetic maps and genome assemblies can prove challenging because genetic markers are commonly derived from transcribed sequences that are incompletely and variably annotated. We developed the program MapToGenome as a tool for comparing transcript maps and genome assemblies. MapToGenome processes sequence alignments between mapped transcripts and whole genome sequence while accounting for the presence of intronic sequences, and assigns orthology based on user-defi ned parameters. To illustrate the utility of this program, we used MapToGenome to process alignments between vertebrate genetic maps and genome assemblies 1) self/self alignments for maps and assemblies of the rat and zebrafi sh genome; 2) alignments between vertebrate transcript maps (rat, salamander, zebrafi sh, and medaka) and the chicken genome; and 3) alignments of the medaka and zebrafi sh maps to the pufferfi sh (Tetraodon nigroviridis) genome. Our results show that map-genome alignments can be improved by combining alignments across presumptive intron breaks and ignoring alignments for simple sequence length polymorphism (SSLP) marker sequences. Comparisons between vertebrate maps and genomes reveal broad patterns of conservation among vertebrate genomes and the differential effects of genome rearrangement over time and across lineages.

Original languageEnglish
Pages (from-to)15-25
Number of pages11
JournalEvolutionary Bioinformatics
StatePublished - Feb 14 2007

Bibliographical note

Publisher Copyright:
© 2007, Libertas Academica Ltd. All rights reserved.


  • Comparative genomics
  • Gapped alignment
  • Linkage
  • Transcript map

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Computer Science Applications


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