DRACO

Direct Repeat Aware Codon Optimizer for TAL effectors:

DRACO aims to ease the design and synthesis of gene fragments encoding for highly repetitive protein sequence, such as TALE DNA binding domains by utilizing repeat-aware codon optimization.

usage: draco [-h] [--upstream UPSTREAM] [--downstream DOWNSTREAM]
             [--avoid AVOID] [--prepend PREPEND] [--append APPEND]
             [--check-repeats CHECK_REPEATS] [--repeat-len REPEAT_LEN]
             [--check-inv-repeats CHECK_INV_REPEATS]
             [--inv-repeat-len INV_REPEAT_LEN] [--check-stretch CHECK_STRETCH]
             [--stretch-len STRETCH_LEN] [--check-gc CHECK_GC]
             [--max-gc MAX_GC] [--gc-window GC_WINDOW]
             [--repeat-attempts REPEAT_ATTEMPTS] [--seq-attempts SEQ_ATTEMPTS]
             [--handicap HANDICAP] [--progress] [--log LOG] [--debug DEBUG]
             sequence

Direct Repeat Aware Codon Optimizer

positional arguments:
  sequence              TALE binding sequence (DNA)

optional arguments:
  -h, --help            show this help message and exit
  --upstream UPSTREAM   Protein sequence to include upstream of the repeats
  --downstream DOWNSTREAM
                        Protein sequence to include downstream of the repeats
  --avoid AVOID         Avoid this fragment in the optimized sequence (can be
                        specified multiple times)
  --prepend PREPEND     Prepend the optimized sequence with this DNA sequence
                        (this fragment won't be optimized)
  --append APPEND       Append this DNA sequence to the optimized sequence
                        (this fragment won't be optimized)
  --check-repeats CHECK_REPEATS
                        Check the optimized sequence for repeats
  --repeat-len REPEAT_LEN
                        Max allowed length of a repeat
  --check-inv-repeats CHECK_INV_REPEATS
                        Check the optimized sequence for inverse repeats
  --inv-repeat-len INV_REPEAT_LEN
                        Max allowed length of an inverted repeat
  --check-stretch CHECK_STRETCH
                        Check for base stretches
  --stretch-len STRETCH_LEN
                        Max allowed length of a base stretch
  --check-gc CHECK_GC   Check GC content
  --max-gc MAX_GC       Max allowed GC content
  --gc-window GC_WINDOW
                        GC calculation window
  --repeat-attempts REPEAT_ATTEMPTS
                        Max attempts to optimize a repeat
  --seq-attempts SEQ_ATTEMPTS
                        Max attempts to optimize the sequence
  --handicap HANDICAP   Max codon handicap for the optimized sequence
  --progress            Show progress indicator
  --log LOG             Logging level
  --debug DEBUG         Enable debug logging