Run the two gfServer commands to start the blat servers:
gfServer start localhost 17777 -trans -mask araTha1.2bit &
gfServer start localhost 17779 -stepSize=5 araTha1.2bit & STEP 8. Load this plant assembly hub by using this URL and selecting it under the "group" category where "Plant araTha1" displays:
http://127.0.0.1:1234/cgi-bin/hgGateway?genome=araTha1&hubUrl=http://127.0.0.1:1234/folders/hubExamples/hubAssembly/plantAraTha1/hub.txt
On the blat page, http://127.0.0.1:1234/cgi-bin/hgBlat, you can now select the
Arabidopsis thaliana assembly and blat plant amino acid sequences, like
IYQTRENKYIIGEIQITESERDRRRSSLPGNH
or DNA sequences, like TAAGTAAAAAATAATATGATTAAGACTAATAAATCTTAATAGTTAATACT.
-
+
On the PCR page, http://127.0.0.1:1234/cgi-bin/hgPcr, you can now select the
+Arabidopsis thaliana genome and enter a forward primer such as
+TAGGTCTGCACCTGTGGTTCAAAATTTT and a reverse primer such as
+CAATACAAGTCAACATTTTAGCGCCGAGA and click the "Flip Reverse Primer"
+box and then click submit to find matches on the assembly.