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
