Hello all,

Did this issue get resolved?

If Sandrine was right about there being an off by one error in GI number in
the BLAST tabular output, it could be a bug in 'legacy' blastall command.

I say 'legacy' BLAST because that's what Galay's NGS 'megablast' tool
is using internally (as opposed to the the NCBI's replacement BLAST+).

Peter

On Wed, Jan 25, 2012 at 3:14 PM, Guru Ananda <g...@psu.edu> wrote:
> Dear Sandrine,
>
> Thanks for pointing out this issue.
> The BLAST databases we have on Galaxy are from last year, while those on
> NCBI website are the latest (Jan 2012). As pointed out on NCBI website
> (http://www.ncbi.nlm.nih.gov/Sitemap/sequenceIDs.html), it appears that each
> time any change is made to a sequence/database, GI numbers change as well.
> This is perhaps why you're observing discrepancies in GI numbers and lengths
> between megablast outputs on Galaxy and NCBI. I'm currently in the process
> of downloading the latest BLAST databases from NCBI, and I'll let you know
> when they're available for use on Galaxy.
>
> Thanks for your patience,
> Guru
> Galaxy team.
>
>
> On Wed, Nov 9, 2011 at 8:03 AM, Sandrine Hughes
> <sandrine.hug...@ens-lyon.fr> wrote:
>>
>> Dear all,
>>
>> I’m not sure where I need to send my email so I apologize if I’m wrong.
>>
>> I have a trouble with the Megablast program available in NGS Mapping and I
>> hope that you can help. Indeed, I think that there might be a problem with
>> the table given in output, and notably a shift between the GI numbers and
>> the parameters associated.
>>
>> Here are the details:
>>
>> I. First, what I have done :
>>     I used the program to identify the species that I have in a mix of
>> sequences by using the following options:
>>             Database nt 27-Jun-2011
>>             Word size 16
>>             Identity 90.0
>>             Cutoff 0.001
>>             Filter out low complexity regions Yes
>>     I run the analyses twice and obtained exactly the same results (I used
>> the online version of Galaxy, not a local one).
>>
>> II. Second, I analysed the data obtained for one of my sequence (1-202).
>> The following lines are the beginning of the table that I obtained after the
>> megablast and two lines with troubles:
>>
>>  1-202   312182292       484     99.33   150     1       0       1
>>       150     1       150     2e-75   289.0
>>  1-202   312182201       476     99.33   150     1       0       1
>>       150     1       150     2e-75   289.0
>>  1-202   308228725       928     99.33   150     1       0       1
>>       150     19      168     2e-75   289.0
>>  1-202   308228711       938     99.33   150     1       0       1
>>       150     22      171     2e-75   289.0
>>  1-202   308197083       459     99.33   150     1       0       1
>>       150     10      159     2e-75   289.0
>>  1-202   300392378       920     99.33   150     1       0       1
>>       150     10      159     2e-75   289.0
>>  1-202   300392376       918     99.33   150     1       0       1
>>       150     9       158     2e-75   289.0
>>  1-202   300392375       922     99.33   150     1       0       1
>>       150     11      160     2e-75   289.0
>>  1-202   300392374       931     99.33   150     1       0       1
>>       150     21      170     2e-75   289.0
>>  1-202   300392373       909     99.33   150     1       0       1
>>       150     21      170     2e-75   289.0
>>  1-202   300392371       1172    99.33   150     1       0       1
>>       150     9       158     2e-75   289.0
>> ...
>> 1-202   179366399       151762  98.67   150     2       0       1
>>       150     46880   47029   6e-73   281.0
>> 1-202   58617849        511     98.67   150     2       0       1
>>       150     21      170     6e-73   281.0
>>
>>
>> III. Third, what I’ve noticed:
>>     My first trouble was that among all the species identified, two were
>> very different from the expected ones (2 last lines). So I decided to search
>> if that could be possible for that sequence and performed independently a
>> megablast on the NCBI with similar options. I was not able to find these two
>> species in the results.
>>     So, I decided to check the hits identified in the table above and
>> identified a second trouble. In the table, the second column give the GI of
>> the database hit and the third column give the length of the database hit.
>> However, when I manually checked in NCBI the length of the GI, this one was
>> incorrect. Indeed, for the GI 312182292, the length should be 580 and not
>> 484.
>>     By checking different lines, I noticed that the length that is given
>> for a GI corresponds to the length of the GI-1. As you can see in the above
>> table, some GI are consecutive (300392376, 300392375,...). When checking the
>> length of 300392376 in NCBI, I should have 920. But when I checked
>> 300392375, I found 918. And this was true for the following lines :
>> 300392374 give normally 922 and 300392373 give 931... My conclusion at that
>> point was that there was a shift of –1 between the GI and the other
>> parameters of the line (indeed the parameters for the remaining columns are
>> in agreement with the length of the GI-1). However, that’s not always
>> true.... For some GI given in the table (for example, the two last lines),
>> if we check the parameters of the GI-1, the parameters are completely
>> different... So, I suppose that there is a trouble in the GI sorting during
>> the megablast but I’m not able to clearly define the problem.
>>
>> IV. Fourth, confirmed with an other dataset
>>     In order to be sure that the problem was not linked to my data or my
>> process, I asked a colleague to do a megablast on independent data. The
>>  conclusions were similar to mine : a shift in the GI given in the table and
>> the parameters associated, that most of the time but not always, correspond
>> to GI-1.
>>
>> Can you confirm that there is a problem with the output of the megablast
>> available in Galaxy ? If yes, do you think you can fix it ?
>>
>> Many thanks for your help,
>>
>> Best regards,
>>
>> Sandrine
>
>
>
>
> --
> Graduate student, Bioinformatics and Genomics
> Makova lab/Galaxy team
> Penn State University
> 505 Wartik lab
> University Park PA 16802
> g...@psu.edu
>
>
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