So, Jen, I'm not sure if we're talking about the same ID change... I
am under the impression that GenBank does not change it's GI numbers
for it's entries. Plus, it's now looking like all sequence length
output info for each hit through Galaxy's megablast does not match to
the GI number output given by Galaxy megablast, but to the GI number
before it. Because the "-1" rule is so consistent, it makes this seem
less and less like it has to do with NCBI changing it's GI numbers to
make room for new entries or something. In other words, there is a
shift, as if a 1 was added to each NCBI GI number in galaxy before
galaxy produces the output file.

I need someone to tell me if I can trust the output. Basically I see
it this way. Every hit row from Galaxy megablast actually has
information for two NCBI entries: the one that shares the GI output
and the one before it that shares the sequence length output. Which
one is the hit I should be using?
Because on some occations, the NCBI entry that shares the GI output
from galaxy is VERY distantly related to the NCBI entry that shares
the subject sequence length output from galaxy, and I don't know which
to pick. Is this problem well understood, yet?

On Tue, Apr 24, 2012 at 10:52 AM, Peter Cock <> wrote:
> On Mon, Apr 23, 2012 at 11:41 PM, Sarah Hicks <> wrote:
>> Peter, you requested an example, here are the first five hits for my
>> first query sequence (OTU#0)
>> 0       324034994       527     93.23   266     13      5       1       265  
>>    22      283     7e-102  379.0
>> 0       56181650        513     93.26   267     10      8       1       265  
>>    25      285     7e-102  379.0
>> 0       314913953       582     91.79   268     13      9       1       265  
>>    24      285     2e-92   347.0
>> 0       305670062       281     92.52   254     14      5       4       256  
>>    32      281     2e-92   347.0
>> 0       310814066       1180    91.73   266     14      7       1       265  
>>    24      282     9e-92   345.0
>> You will notice there are 13 columns, one in addition to the 12 column
>> titles you explained. This is because there is a column between sseqID
>> and pident.
> I see now - the calls megablast (from the old legacy
> NCBI blast suite) which does indeed produce 12 column tabular output. But
> the wrapper script then edits the output:
> It appears to be splitting column 2 in two at the underscore intended to
> give the match ID and the length. This puzzles me but I haven't used
> the legacy BLAST tabular output for a while. On BLAST+ you can ask
> for the query or subject length explicitly as their own columns so we
> don't have this problem.
> The also re-formats the floating point score in the
> last column, apparently the NCBI style could cause problems with the
> Galaxy filter tool.
>> In the metagenomic tutorial the first 4 columns are
>> explained, and column 3 is described as length of sequence in database
>> (or length of the subject sequence).
>> This is the problem column. The length of only one of the subject GI
>> numbers above match the subject length in NCBI. This has caused me to
>> wonder if I can trust the hit info. In all cases that I've checked,
>> when this happens the correct match is the listed GI value minus 1
>> (ie, in NCBI, gi|324034994 is not 527nt long, but 324034993 IS 527nt
>> long).
> That is strange.
> Peter

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