[Genome] novel peptide

[Brooke Rhead]

Hello Bing,

If you already know which known peptides you would like to compare the 
novel peptides against, you can look them up in our Proteome Browser, here:

http://genome.ucsc.edu/cgi-bin/pbGateway

If you need to determine where your peptides align to the genome, you 
can use the BLAT tool (hit the "Blat" link at the top of the page, or 
just use this link: http://genome.ucsc.edu/cgi-bin/hgBlat).  Then you 
can compare your peptides to any genes that are annotated in the regions 
where the peptides align.  Note that we do not have any tracks that only 
show peptides -- you will need to look at the tracks under "gene and 
gene prediction tracks".  Many of these tracks have more information 
about associated proteins on their details pages (which you see when you 
click on the individual items in the track).  Note that the "UCSC Genes" 
track contains links directly to the Proteome Browser.

I hope this information helps.  If you have further questions, please do 
not hesitate to write back to this list.

--
Brooke Rhead
UCSC Genome Bioinformatics Group


杨兵 wrote:
> Hi all,
> 
> 
> 
>      We have identified 29 high confidence novel peptides which didn't
> contain in IPI human protein database. We want to compare these peptides
> with the human genome annotation for finding whether our peptides matched
> with the exons. We want to know whether our peptides represent novel
> alternative forms or sequence polymorphisms. How to do these by using genome
> browser? Thanks for your help in advance.
> 
> 
> 
> Sincerely,
> 
> Bing Yang
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome