Dear Jennifer: Thank you so much for your quick response. I think these are helpful, and I just checked the NCBI ftp site to find out the most current honey bee RNA sequence, which it was updated in October 2006.
However, I still have problem to ask for your help. In my analysis, I want to extract the genomic sequence(which includes both intron and exon) for a bunch of genes. I know in UCSC Genome Browser it is very easy to do that because there are many options for you such as 5'UTR Exon,3'UTR Exon, CDS Exon,Intron, to select. But in NCBI I can only get the mRNA sequence for a certain refseq ID instead of the whole gene sequence. I think if I make a custom track in UCSC genome browser from NCBI, I still can't extract the sequence like I mentioned above. Do you have any idea to extract the sequence as what I need based on the most current information from NCBI? Thank you. Jia Zeng ----- Original Message ----- From: "Jennifer Jackson" <[email protected]> To: [email protected] Cc: [email protected] Sent: Tuesday, August 18, 2009 1:25:45 PM GMT -05:00 US/Canada Eastern Subject: Re: [Genome] question about honey bee NCBI gene track Hello, This is likely related to updates between our version of the track and the data at NCBI. For apiMel2, the NCBI Gene Model track's description page notes that: Data last updated: 2005-05-26 There may have been updates since then - check at NCBI. If you want to, the entire current dataset could be extracted from NCBI, formatted as a custom track, and uploaded. Instructions for data formats, custom tracks, and other tools are in our FAQ. If you need help locating something specific, please let us know. Thanks, Jen ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- [email protected] wrote: > From: [email protected] > To: [email protected] > Sent: Tuesday, August 18, 2009 9:18:44 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] question about honey bee NCBI gene track > > Dear Genome: > > I am using UCSC genome browser to do some analysis about honey > bee(A.mellifera) genome. For my purpose, I use the NCBI Genes track > under A.mellifera genome. However, when I manually check the sequence > for a same refseq ID between UCSC and NCBI, I found there were always > some difference among them. The attach file is a sequence alignment > for XM_392354 between the resources I mentioned above. Because my > analysis is very sensitive to the length of gene. Could you tell me > why there is difference between the same refseq gene from different > resources and what resource is the most current one? Thank you very > much > > Jia Zeng > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
