Hi James, I still don't have a good answer for your original question, but if you are having trouble using BLAT because the sequences are too short, you might try turning on the "Short Match" track at UCSC (in the Mapping and Sequencing Tracks section). It will display exact matches of 2-30 bases in length on the main display page of the Genome Browser (you will need to actually look at each chromosome in the browser to see results, though).
Also, if you are comfortable running command-line tools you may be interested in the oligoMatch utility in the source tree (available here: http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads), which can also be used to find perfect sequence matches. The assembly .2bit files to use with the tool are available here: http://hgdownload.cse.ucsc.edu/downloads.html (under the "Full data set" links). -- Brooke Rhead UCSC Genome Bioinformatics Group On 08/17/11 06:35, Zadina, James E wrote: > The NCBI Genome blast searches produce hits in contig coordinates as > below > > But and USC genome browser and the NCBI Mapviewer use chromosome > coordinates. > > Is there a utility to batch convert contig to chromosome coordinates? > > > > e.g. if I condense the hits to a list of contig coordinates of the > target/subject sequences something like the below, > > Can I get output in chromosome coordinates? > > Or can I somehow (not obvious to me) request chromosome coordinates when > running the BLAST? > > > > 1. ref|NT_011651.17| > <http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?maps=blast_set&db=ref_cont > ig&na=1&gnl=ref%7CNT_011651.17%7C&gi=224514715&term=224514715%5Bgi%5D&ta > xid=9606&RID=4EA5DVWY01P&QUERY_NUMBER=1&log$=nuclalign> > Length=36813976..... Sbjct 33290942 XXXXXX 33290928 > > 2. ref|NT_011651.17| > <http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?maps=blast_set&db=ref_cont > ig&na=1&gnl=ref%7CNT_011651.17%7C&gi=224514715&term=224514715%5Bgi%5D&ta > xid=9606&RID=4EA5DVWY01P&QUERY_NUMBER=1&log$=nuclalign> Length........ > > : > > : > > > > Thanks > > J > > > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
