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FSPLICE

FSPLICE - find splice sites in genomic DNA

Paste nucleotide sequence here:

Alternatively, load a local file with sequence in Fasta format:

Local file name:

Select organism specific gene-finding parameters :

Total 539 genome-specific parameters are available for genefinders of FGENESH suite

Search in chain:  Direct
 Reverse
 Both

Search for GC donor site 

Output splice site sequence 
Output splice site sequence length 

Splice site threshold 

Advanced options [see example of value in (..)]:

Use condensed sequence.
Get sequence from this position.
Get sequence to this position (if 0, then to the sequence end).
Print position as in origin (not cut sequence).
Print site wight distribution for selected splice site types.
Set threshold for all sites (floating point number).
Set threshold for AG sites, to find more then N percent of true sites.
Set threshold for AG sites (floating point number).
Set threshold for GT sites, to find more then N percent of true sites.
Set threshold for GT sites (floating point number).
Set threshold for GC sites, to find more then N percent of true sites.
Set threshold for GC sites (floating point number).
Add AG site to selection.
Remove AG site from selection.
Add GT site to selection.
Remove GT site from selection.
Remove GC site from selection.
Put here other options, if any.

[Help] [Hide advanced options
[Example]

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Most gene finding parameters presented here were trained by Softberry for its own use and distribution, using proprietary and publicly available data. Some of the parameters were created for our academic customers, including Broad Institute/MIT, Washington University, University of Minnesota and The Institute for Genomic Research (TIGR).


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Last modification date: 12 Dec 2013