Hi James, We do not have the "NT_" coordinates in the UCSC Genome Browser. If you can use BLAT (http://genome.ucsc.edu/cgi-bin/hgBlat) instead of BLAST, you will be able to see the results in the Genome Browser, and you will get chromosome coordinates instead of contig names in your output. Otherwise, I suggest asking NCBI about a way to convert BLAST output to chromosome coordinates.
-- Brooke Rhead UCSC Genome Bioinformatics Group On 08/14/11 10:01, Zadina, James E wrote: > NCBI Genome blast searches produce hits in contig coordinates > > Is there a utility to batch convert to chromosome coordinates? > > e.g. if I condense the hits to a list of contig coordinates of the > subject something like: > > > > 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 33290928 > > 2. ..... > > > > Can I get output in chromosome coordinates? > > > > 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
