SeedChooser: seed evaluation and recommendation tool
(contact: whchung@sejong.knu.ac.kr)
seedchooser: the main program which recommends a good seed by following the parameters.
seedevaluator: the program which evaluates a set of the input seeds.
oligogenerator: the program to generate a set of oligos following the experimental conditions.
Installation
Operating system(s):
Window XP (and above), Linux (Ubuntu, Redhat, etc.)
* Current, the programs are only tested on Microsoft Windows Family.
Required programs:
- Python version 2.3 or above (available at http://www.python.org/download/)
- Programs for oligogenerator
n CLUSTALW (available at http://www.ebi.ac.uk/Tools/clustalw/index.html)
n UNAFOLD (available at http://dinamelt.bioinfo.rpi.edu/download.php)
- Caution: above programs should be in the system path.
Download (version 0.3)
Quick start
Unzip the downloaded zip file
> cd ./seedchooser
l SeedChooser
> python seedchooser.py –o sample.oligo
l SeedEvaluator
> python seedevaluator.py –o sample.oligo –s test.seed
l OligoGenerator
> python oligogenerator.py –o sample.oligo
Usage
seedchooser
Usage: seedchooser.py -o OLIGO [options]
Options:
-h, --help show this help message and exit
-o OLIGO, --oligo=OLIGO
read oligo samples from OLIGO file
-n NUMBER, --number=NUMBER
number of trials to find the optimal seeds
-w WMIN, --weight-min=WMIN
minimum seed weight
-W WMAX, --weight-max=WMAX
maximum seed weight
-r REPORT, --report=REPORT
write the report to REPORT file (if not, print the
report to stdout)
-a ALPHA, --alpha=ALPHA
parameter for discriminability (if a > 1, precision >
recall; if 0 < a < 1, precision < recall)
-b BETA, --beta=BETA parameter for efficiency (penalty for redundant
hashing)
-g GAMMA, --gamma=GAMMA
parameter for efficiency (penalty for redundant oligo
selection)
-v, --verbose print status messages to stdout
seedevaluator
Usage: seedevaluator.py -o OLIGO -s SEED (or -p PRDA) [options]
Options:
-h, --help show this help message and exit
-o OLIGO, --oligo=OLIGO
read oligo samples from OLIGO file
-s SEED, --seed=SEED read test seeds from SEED file
-p PRDA, --prda=PRDA read PRDA info from PRDA file (it disables -o and -s
options)
-r REPORT, --report=REPORT
write evaluation report to REPORT file (if not, print
the report to stdout)
-a ALPHA, --alpha=ALPHA
parameter for discriminability (if a > 1, precision >
recall; if 0 < a < 1, precision < recall)
-b BETA, --beta=BETA parameter for efficiency (penalty for redundant
hashing)
-g GAMMA, --gamma=GAMMA
parameter for efficiency (penalty for redundant oligo
selection)
-v, --verbose print status messages to stdout
oligogenerator
Usage: oligogenerator.py -o OLIGO [options]
Options:
-h, --help show this help message and exit
-l LENGTH, --length=LENGTH
oligo length
-n NUMBER, --number=NUMBER
number of oligos
-s SAMPLING, --sampling=SAMPLING
number of the variants sampling from an oligo
-o OLIGO, --oligo=OLIGO
write the generated oligos to OLIGO file
-M MELT, --Melt=MELT melting temperature for calculating free energy
-I IDENT_THRES, --ident=IDENT_THRES
threshold of sequence identity to check cross-
hybridization
-C CONT_THRES, --cont=CONT_THRES
threshold of the length of continuous match to check
cross-hybridization
-F FREE_THRES, --free=FREE_THRES
threshold of the reverse of free-energy to check
cross-hybridization
-v, --verbose print status messages to stdout
File format
.oligo : a file format which is generated from OligoGenerator.
.seed : a file format which contains the seed information to test.
.prda : an intermediate file format which is generated from SeedEvaluator.
.out : an output file format of either SeedChooser or SeedEvaluator.