1. What should I do if I can't find the species that I am interested in from the list?
If you don't see your taxon of interest in the list, please select the query and/or subject species that
are closely related to your species or whose taxonomic range covers your species. For example, if you are
interested in a fish species that is not listed, you can select other fishes for searching. More genomes will
be added into the next version of EvolMarkers. Please fill out the Suggestion Form,
if you'd like your favorite species to be added to the next version of EvolMarkers.
2. Should I use one or more subject taxa? What's the difference?
Using more related subject taxa could return more sequences for primer design, which should be helpful for
designing universal primers. But you may also get fewer markers.
3. Why I got so few markers from the search? How can I improve it?
This could be due to a few different causes. Maybe the genetic distance is too larger between the query and
subject taxa, so few homologous markers exist. Sometimes, the genome data have low coverage and little
annotations, which may lead to fewer markers identified. With the limited resources, you can lower the
criteria, such as the minimum size of the CDS, or you can pick a well-annotated genome as the query. Starting
search with different queries and combining the results may also increase the number of markers found.
Eventually, with more and more genomes being sequenced and annotated, we should expect getting more markers.
4. How do I know the size of the intron of the EPIC in my species?
The number appended in the end of each sequences in the fasta files of EPIC markers indicates the size of
intron. Because the sequences of subject species are retrieved according to the BLAST results, the intron
size listed for the subject species is not exact but close. If you used EST data as the subject, the
numbers calculated for those species are not indicates for intron size, because there are no intron sequence
information in EST data. More important, if your species of interest is not the query or subject species,
the intron size should be found out experimentally. Because intron size can vary a lot even between closely
related species (e.g., sister genera), the intron size in one species has little value for predicting the
intron size in another species.
For questions, please contact Chenhong Li
(lichenhong.unl@gmail.com).
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