On Mon, Apr 23, 2012 at 5:56 PM, Sarah Hicks <garlicsc...@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

The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:


To manage your subscriptions to this and other Galaxy lists,
please use the interface at:


Reply via email to