On Mon, Apr 23, 2012 at 5:56 PM, Sarah Hicks <garlicscape@gmail.com> wrote:
I am having trouble finding information on the MegaBLAST output columns. What is each column for? I can't seem to figure this out by comparing info in the columns to NCBI directly because the GI#'s don't match with the correct entry on NCBI. I've seen that others have posted about that problem, so I'm also waiting on details on that question, but for now, I'd just like to know what to make of the output... best, Sarah
I've not tried to track down this reported possible bug in GI numbers, and weather it also affects BLAST+ as well as the legacy NCBI BLAST (which has now been discontinued). Do you have a specific example. As to the 12 columns, they are standard BLAST tabular output, and should match the defaults in BLAST+ tabular output which are: Column NCBI name Description 1 qseqid Query Seq-id (ID of your sequence) 2 sseqid Subject Seq-id (ID of the database hit) 3 pident Percentage of identical matches 4 length Alignment length 5 mismatch Number of mismatches 6 gapopen Number of gap openings 7 qstart Start of alignment in query 8 qend End of alignment in query 9 sstart Start of alignment in subject (database hit) 10 send End of alignment in subject (database hit) 11 evalue Expectation value (E-value) 12 bitscore Bit score Peter