Hello,
All of the sequences that considered for alignment are retained in the
table gbCDnaInfo and gbStatus (even if they do not align).
Sample mySQL query vs gbStatus to get count:
select count(*) from gbStatus where type = "EST" and orgCat =
"native" and numAligns = 0;
Modify the query to output IDs (using the public mySQL server) or use
your own tools versus the text file version after obtaining them from
the Downloads server (ftp/rsync).
Public mySQL:
http://genome.ucsc.edu/FAQ/FAQdownloads.html#download29
Data downloads:
http://genome.ucsc.edu/FAQ/FAQdownloads.html#download1
http://hgdownload.cse.ucsc.edu/downloads.html
http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#Download
For the most recent human and mouse, the data would be here:
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/
http://hgdownload.cse.ucsc.edu/goldenPath/mm9/database/
Jennifer
---------------------------------
Jennifer Jackson
UCSC Genome Informatics Group
http://genome.ucsc.edu/
On 3/14/10 11:43 AM, Erez Levanon wrote:
> Hi
>
> Many problematic ESTs and mRNAs are rejected during their alignments to the
> genome (e.g less than 96% base identity with the genomic sequence). I wonder
> where/if can i find a list of those ESTs (in human and mouse) as we are
> interested in such sequences.
>
> Thanks
>
> Erez
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
