Sequence profiles

eFindSite employs sequence profiles constructed by either SP3 or Sparks. If you use eThread for threading, the target sequence profile is saved as a *.prf file as described in this section of the eThread tutorial. If you use any other threading algorithm, follow these steps to construct a sequence profile for your target:

1. Download SP3/Sparks from http://sparks.informatics.iupui.edu/hzhou/anonymous-fold-sparks2.html and follow installation instructions.

2. Make the following exports:

[example]$ export sparks=/usr/local/sparks

[example]$ export SPARKSDIR=$sparks

This assumes that SP3/Sparks is installed in /usr/local/sparks. If you use a different location, change the path accordingly.

3. Run genfreq script included in SP3/Sparks for the target sequence, e.g. 13gsA.fasta:

[example]$ $sparks/bin/genfreq 13gsA.fasta $SPARKSDIR

Among other output files, you should see 13gsA.prf, which is a sequence profile you can use in eFindSite.

 

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