Hi,
Can anyone please explain me how to use Genscan tool to find exons and introns for a given gene sequence? I want to calculate sensitivity and specificity to check its performance for a given gene sequence.
Thank you in advance
Thank you sir for quick and positive reply and wish you a happy new year-2020
Explanation to understand GENSCAN tool
Gn.Ex : gene number, exon number (for reference)
Type : Init = Initial exon (ATG to 5' splice site)
Intr = Internal exon (3' splice site to 5' splice site)
Term = Terminal exon (3' splice site to stop codon)
Sngl = Single-exon gene (ATG to stop)
Prom = Promoter (TATA box / initation site)
PlyA = poly-A signal (consensus: AATAAA)
S : DNA strand (+ = input strand; - = opposite strand)
Begin : beginning of exon or signal (numbered on input strand)
End : end point of exon or signal (numbered on input strand)
Len : length of exon or signal (bp)
Fr : reading frame (a forward strand codon ending at x has frame x mod 3)
Ph : net phase of exon (exon length modulo 3)
I/Ac : initiation signal or 3' splice site score (tenth bit units)
Do/T : 5' splice site or termination signal score (tenth bit units)
CodRg : coding region score (tenth bit units)
P : probability of exon (sum over all parses containing exon)
Tscr : exon score (depends on length, I/Ac, Do/T and CodRg scores)
Comments
The SCORE of a predicted feature (e.g., exon or splice site) is a log-odds measure of the quality of the feature based on local sequence
properties. For example, a predicted 5' splice site with score > 100 is strong; 50-100 is moderate; 0-50 is weak; and
below 0 is poor (more than likely not a real donor site).
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