This choice will determine, against which
reference genome the designs will be tested.
Minimum length of the nucleotide sequence one arm of the TALEN dimer should recognize.
Maximum length of the nucleotide sequence one arm of the TALEN dimer should recognize.
Length of the sequence that is to be saved 3' to the cut site.
Length of the sequence that is to be saved 5' to the cut site.
Check if designs shell be exclusively hitting some gene found in the database.
In consequence, genes that are not annotated we be excluded.
Check if designs shell be exclusively hitting exons found in the database.
Check to make designes hit exclusively outside of predicted CpG islands.
(Outside potential hypermethylated regions)
Put a number such as 1 to find designs exclusively hitting a specific exon.
Or the word any to find designs that hit any exon.
Put a Transcript ID such as ENST00000369985 to find designs exclusively hitting a specific transcript.
Or the word any to find designs that hit any transcript.
This function is only implemented for single gene analyses.
Check this box to make the program find and save the genomic sequence up- and downstream off the intended cut side.
In case this exceeds the gene length in the database,the stored sequence will be shorter.
If this is checked, the program will asses if there is a unique restriction enzyme recognition site in the spacer region of the TALEN design.
If this box is checked, the programm will test if and what restriction sites are in the TALEN and its surrounding sequence.
Having this box checked tells the programm to assess restricion enzyme cut sites in the whole target sequence.
Choose between different pre-defined restriction enzyme subsets.
In the following subsection, the tool kit used for TALEN assembly is specified .
This choice will inlfuence which alphabet is used to translate the nucleotide sequences
into RVD sequences and the allowed TALEN lengths.
Voytas Lab Golden Gate TALEN Kit: G => NN or NK, with length from 11 to 30 RVDs
Voytas Lab Golden Gate TALEN Kit 2.0:G => NN or NK or NH, with length from 11 to 30 RVDs
Hornung Lab LIC TAL Effector Assembly Kit: G => NK, with length of 18 RVDs
Joung Lab TAL Effector Engineering Reagents (FLASH assembly): G => NN, with length from 8 to 20 RVDs
Zhang Lab TALE toolbox: G => NN, with length from 18 to 20 RVDs
It can be specified if the TALEN designs
should be checked for any secondary off-target effects.
This means if they will cut in any exogenous, foreign introduced sequence.
Check every individual off-target or paste a set of FASTA sequences into the text area
This text area only accepts FASTA format sequences as input e.g.:
>some sequence
ATATCGATGCTAGCTAGCT
GATCGTAGCTAGCTAGCTA