Comparative Genomics

VectorBase genome browser displays precomputed:

  • Protein comparisons, these are done for all genes in all VectorBase genomes. These alignments are the input to generate the gene trees. With the gene trees we can infer homologous relationships, paralogues and orthologues genes.
  • DNA comparisons, these are done for the closely-related (selected genome) species, these are pairwise genome alignments for both coding and non-coding regions, not ideal for fragmented genomes.

These precomputed analyses are run using the 'compara pipeline', the gene tree compara pipeline is re-run every release if at least one of the VectorBase genomes has an updated or new gene set.

If you need additional information, remember that in the genome browser many display links have question marks next to them (e.g., genomic alignments, gene tree, ortholog and paralog pages in the gene tab and, on the alignments and region comparison in the location tab), these are links with more documentation. The following are some sample links:

We have also written some FAQs about this topic:

Browser:

Compara:

If you want to discuss any issues raised in this tutorial then please contact the help desk.

If you are not able to view the YouTube video below, click here to watch the video on youku. Similarly, if you can not access its Google Slides, click the link below to download the slides directly from VectorBase.

These are the slides used in the video tutorial shown above.

Creative Commons License

All VectorBase help and documentation materials have a Creative Commons Attribution-ShareAlike 4.0 International License.