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.