|TALEN target finder M|
|Find TALEN targets on the genome|
|The TALEN target finder M identifies potential target sites of a given TALEN
configuration on the genome. The TALEN target finder M makes a search with a complete TALEN configuration composed of a left and a right TALEN sequence
and a spacer in between by using a position-specific scoring matrix. The search is also done with homodimers
of the left or the right TALEN sequence on both genomic strands. Both the sense and anti-sense strand of the genome
is searched for potential target sites.|
The TALEN target finder M uses the scoring system according to Moscou and Bogdanove (2009) (PMID:19933106) with a correction coefficient for unknown RVD-nucleotide associations of 0.92. The TALEN target finder M uses observed association frequencies for the following RVDs: NI (A), NG (T), NN (G), HD (C).
To submit TALEN sequences you can paste one or multiple TALENs into the window or submit one or multiple TALENs in a plain text file.
Use the following format to submit the TALEN sequences:
TALEN1 sequence, spacer length lower limit, spacer length upper limit, TALEN2 sequence (comma-separated!, one TALEN per line)
The files can be prepared with Excel and exported as .csv file. Select a genome sequence and put your email address in the given field.
The p-value can be modified, but the default value of 1.0E-6 is highly recommended. The score threshold determines how many target hits are displayed in the result files. A value of 20 is a good starting point. More results will be displayed, if the value is decreased to 18 or 16. A value of 1 will bring up all genomic hits, but can result in several hundred thousands of hits and huge result files. A value of 1 is therefore NOT recommended. A threshold of greater than 20 is also not recommended as it could result in a suppression of important target hits.
As result you will receive two files by email:
1. A |-separated text file with the following columns:
talen number|finger print|input sequence|score|target site|genomic locus|strand|link to the genomic locus
Important: The left and right TALEN target sites are shown in genomic orientation.
2. An Excel file with the following columns:
target talen1 sequence | spacer length | target talen2 sequence | score | finger print | genomic locus | genomic strand | link to the genomic locus
Important: In the Excel file the target sequences obtained are shown in the original orientation independent of the genomic localization of the target site on the genome. Mismatches are highlighted in red.
The finger print (fp) is an acronym of the pattern found: h+ means that left TALEN target site is located on the sense and the right TALEN target site is located on the anti-sense strand of the genome. h- means that the left TALEN target site is located on the anti-sense and the right TALEN target site is located on the sense strand of the genome. T1-T1 and T2-T2 refers to a homo-dimeric TALEN target site with the left (T1) or the right (T2) TALEN.