Hello Shan, Unfortunately, we will not be able to update the database at this time. Our funding mandate is to target specifically on vertebrate genome development activities. We realize the relationship and importance of this organism with respect to vertebrate genome analysis, but we currently have other priorities that we must focus on.
Concerning the BLAT vs BLAST (JGI uses BLAST) result - if you are able to obtain the genome sequence from the v2 genome, you might consider installing BLAT and running the query on your own server. That might at least help you to locate your gene in the v2 genome. Here is some BLAT help: http://genome.ucsc.edu/FAQ/FAQblat.html We apologize that we cannot help more right now - but please feel free to check back later (in a few months) for an update. Thanks, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 6/1/10 9:33 AM, Shan Gao wrote: > Dear Sir/Madam, > I am student in University of Michigan. I am using UCSC blat to > located my gene mRNA in the amphioxus genome. It's really helpful. > However, I noticed that the amphioxus database in your website is > verion 1, which is the first/old genome database released in 2006. The > JGI has already released a refined version 2 in 2008, which is more > accurate than the old one. I tried to use blat in the JGI website, in > which I can compare my gene sequence with the version 2 genome > sequence. However, their blat result is not shown as in UCSC blat, so > it's really hard to locate my gene. Is it possible to upload the new > version 2 to your website? It will give us more accurate blat results. > Thank you. I am looking forward to your reply. > Yours sincerely, > Shan > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
