1,146
edits
Changes
Jump to navigation
Jump to search
New page: TESS is the [http://www.cbil.upenn.edu/cgi-bin/tess Transcription Element Search System] curated by the University of Pennsylvania. <blockquote> TESS is a web tool for predicting transcri...
TESS is the [http://www.cbil.upenn.edu/cgi-bin/tess Transcription Element Search System] curated by the University of Pennsylvania.
<blockquote>
TESS is a web tool for predicting transcription factor binding sites in DNA sequences. It can identify binding sites using site or consensus strings and positional weight matrices from the TRANSFAC, JASPAR, IMD, and our CBIL-GibbsMat database. You can use TESS to search a few of your own sequences or for user-defined CRMs genome-wide near genes throughout genomes of interest.
</blockquote>
=Citation=
To cite the use of TESS, cite the following [http://www.cbil.upenn.edu/tess/techreports/1997/CBIL-TR-1997-1001-v0.0.pdf technical report]:
<blockquote>
Schug, J. and C.G. Overton. TESS: Transcription element search software on the WWW. Technical Report CBIL-TR-1997-1001-v0.0, Computational Biology and Informatics Laboratory, School of Medicine, University of Pennsylvania, 1997, URL: http://www.cbil.upenn.edu/tess
</blockquote>
or cite the following book chapter:
<blockquote>
Schug, Jonathan,Using TESS to Predict Transcription Factor Binding Sites in DNA Sequence in Current Protocols in Bioinformatics, ed. A.D. Baxevanis. J Wiley & Sons, 2003.
</blockquote>
=Interpreting Results=
Here is the description for the scores returned by TESS. Essentially, sort the Tabular Results using the "La" column to get the best fitting results (i.e. most likely to be real matches of the cis-element with your sequence. ) Those items with an "La/Len" score of 2.0 are perfect fits.
Also, it is presumably a good idea to get p-values less than 0.05 for Lpv, Spv, and Pv, although I'm not sure what that means.
<tab>
La Log-likelihood score, higher is better.
La/ La / Len, higher is better, maximum is 2.0.
Lq La / L_M, where L_M is the maximum La possible for the site model, higher is better, best is 1.0
Ld L_M - La, 0 is best, higher is worse.
L Pv Approximate p-value for La score
Sc Core similarity as reported at TRANSFAC site
Sm Matrix similarity as reported at TRANSFAC site
S Pv Approximate p-value for Sm score
P-v Poisson-model p-value
Model Which site strings or weight matrix was used to pick this site
Factor Which factor(s) does the model represent
</tab>
<blockquote>
TESS is a web tool for predicting transcription factor binding sites in DNA sequences. It can identify binding sites using site or consensus strings and positional weight matrices from the TRANSFAC, JASPAR, IMD, and our CBIL-GibbsMat database. You can use TESS to search a few of your own sequences or for user-defined CRMs genome-wide near genes throughout genomes of interest.
</blockquote>
=Citation=
To cite the use of TESS, cite the following [http://www.cbil.upenn.edu/tess/techreports/1997/CBIL-TR-1997-1001-v0.0.pdf technical report]:
<blockquote>
Schug, J. and C.G. Overton. TESS: Transcription element search software on the WWW. Technical Report CBIL-TR-1997-1001-v0.0, Computational Biology and Informatics Laboratory, School of Medicine, University of Pennsylvania, 1997, URL: http://www.cbil.upenn.edu/tess
</blockquote>
or cite the following book chapter:
<blockquote>
Schug, Jonathan,Using TESS to Predict Transcription Factor Binding Sites in DNA Sequence in Current Protocols in Bioinformatics, ed. A.D. Baxevanis. J Wiley & Sons, 2003.
</blockquote>
=Interpreting Results=
Here is the description for the scores returned by TESS. Essentially, sort the Tabular Results using the "La" column to get the best fitting results (i.e. most likely to be real matches of the cis-element with your sequence. ) Those items with an "La/Len" score of 2.0 are perfect fits.
Also, it is presumably a good idea to get p-values less than 0.05 for Lpv, Spv, and Pv, although I'm not sure what that means.
<tab>
La Log-likelihood score, higher is better.
La/ La / Len, higher is better, maximum is 2.0.
Lq La / L_M, where L_M is the maximum La possible for the site model, higher is better, best is 1.0
Ld L_M - La, 0 is best, higher is worse.
L Pv Approximate p-value for La score
Sc Core similarity as reported at TRANSFAC site
Sm Matrix similarity as reported at TRANSFAC site
S Pv Approximate p-value for Sm score
P-v Poisson-model p-value
Model Which site strings or weight matrix was used to pick this site
Factor Which factor(s) does the model represent
</tab>