Hello,
Is there a limit to the number of sequences that can be used to calculate conservation scores using the Valdar option in the AACon Web Service? I have ~1200 sequences and am unable to retrieve a conservation score. Please help.
Regards,
Hershna
yes. there is a limit - specified as the total number of gaps/residues in the alignment. Unfortunately, Jalview doesn't yet warn you when you've exceeded it (I just added that to our todo list). Sorry about that!
If you are able to install the 'VMWare player' then you could download your own JABA installation from http://www.compbio.dundee.ac.uk/jabaws/ and adjust the configuration file to support conservation analysis for more sequences. The relevant file is conf/settings/AAConLimits.xml (http://source.jalview.org/gitweb/?p=jabaws.git;a=blob;f=conf/settings/AAConLimits.xml;h=6a3b1c2c327dfe2c4085ea948187643a3498051a;hb=refs/heads/JABAWS_Release_2_1_0)
Jim.
On 27/10/2014 15:41, Patel, Hershna wrote:
Hello,
Is there a limit to the number of sequences that can be used to calculate conservation scores using the Valdar option in the AACon Web Service? I have ~1200 sequences and am unable to retrieve a conservation score. Please help.
Regards,
Hershna
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Hi Jim and Hershna,
Maybe it only applies to the consensus score, but when I was having similar problems in July, I got this message in the Jalview Java console:
submission error with calculating Amino acid consensus using AACon service :
compbio.metadata.LimitExceededException: Job exceed size limits, maximum number
of sequences must be less than 5000
and an average sequence length must not exceed 1000
However, the task contained 9684 sequences
and an average sequence length was 552
Apparently, "average sequence length" meant the length of the whole alignment (as Jim said, including gaps). Another problem was that my alignment had a nonstandard residue character (U for selenocysteine). I couldn't get AACon results until I had <5000 sequences and removed all the ones with selenocysteine. You might check for U, O, B, Z, X. Not sure if it matters which scoring method(s) were used… I was trying to calculate all of them!
Best,
Elaine
----------
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
On Oct 27, 2014, at 8:56 AM, Jim Procter <jprocter@compbio.dundee.ac.uk> wrote:
yes. there is a limit - specified as the total number of gaps/residues
in the alignment. Unfortunately, Jalview doesn't yet warn you when
you've exceeded it (I just added that to our todo list). Sorry about that!If you are able to install the 'VMWare player' then you could download
your own JABA installation from http://www.compbio.dundee.ac.uk/jabaws/
and adjust the configuration file to support conservation analysis for
more sequences. The relevant file is conf/settings/AAConLimits.xml
(http://source.jalview.org/gitweb/?p=jabaws.git;a=blob;f=conf/settings/AAConLimits.xml;h=6a3b1c2c327dfe2c4085ea948187643a3498051a;hb=refs/heads/JABAWS_Release_2_1_0)Jim.
On 27/10/2014 15:41, Patel, Hershna wrote:
Hello,
Is there a limit to the number of sequences that can be used to calculate conservation scores using the Valdar option in the AACon Web Service? I have ~1200 sequences and am unable to retrieve a conservation score. Please help.
Regards,
Hershna