Demo 1. Searching for CDS markers in Hymenoptera.

Hymenoptera is one of the largest orders of insect with over 130,000 described species. It includes the sawflies, wasps, bees, and ants. Many of them are economically or ecologically important. Here is an example showing how to search for CDS markers in Hymenoptera. The following options were selected on the searching page. "CDS markers" was checked. The minimum length of CDS was set as 500 (the default was 700). Drosophila melanogaster was chosen as the query, because its genome is well studied. Three Hymenoptera were selected as the subject genomes. Then hit the submit button to start the search. The search may take a few seconds to hours depending on the number of markers found. So please wait patiently and don't click back/forward button.

This search resulted in 42 CDS markers. In the results page, all candidate markers are listed in Drosophila_melanogaster.onehitCDSmarkers.txt. It shows the name of the gene, the position of the markers in each species, average identity, coverage and length of the markers. The CDSmarkers folder has all fasta files for you to download.

Demo 2. Searching for EPIC in bird and Anolis lizards.

The Anolis lizards are one of the best examples to study adaptive radiation and convergent evolution. Nuclear EPIC markers should facilitate such studies. Here is an example of searching for conserved EPIC markers in Anolis lizards. On the searching page, "EPIC markers" was checked. The maximum intron length was left as the default, 1000 bp, which means the intron size must be less than 1 kb in at least one of the species. The identity in flanking exon was set as the default, 85. The number of file to be saved was set as 100, which can be changed if more markers were needed. Gallus gallus was selected as the query, since it has better annotation. Anolis carolinensis and Taeniopygia guttata were used as the subject genomes.

This search produced 1001 EPIC markers. In the results page, All candidate EPIC markers are listed in Gallus_gallus.EPIClist.txt. It includes the name of the markers, the position of the flanking exons for each marker and the intron size. The EPICmarkers folder has fasta files for all EPIC markers for you to download.

In each fasta file, the position of intron is indicated by "XXXXX". Because the sequences of the subject species were retrieved by blasting, their exact intron position might be one or two nucleotides off. The length of intron is the number appended in the end of each sequence. See the following example.

For questions, please contact Chenhong Li (
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