GENSCANW output for sequence 10:52:05 GENSCAN 1.0 Date run: 23-Aug-101 Time: 10:52:06 Sequence sequence : 20000 bp : 40.28% C+G : Isochore 1 ( 0 - 43 C+G%) Parameter matrix: HumanIso.smat Predicted genes/exons: Gn.Ex Type S .Begin ...End .Len Fr Ph I/Ac Do/T CodRg P.... Tscr.. ----- ---- - ------ ------ ---- -- -- ---- ---- ----- ----- ------ 1.01 Init + 1072 1206 135 0 0 73 86 117 0.898 10.19 1.02 Term + 4403 4513 111 1 0 38 41 104 0.796 -1.72 1.03 PlyA + 5437 5442 6 1.05 2.05 PlyA - 5508 5503 6 1.05 2.04 Term - 6297 6139 159 0 0 101 39 108 0.916 4.16 2.03 Intr - 7259 7215 45 2 0 109 58 54 0.748 2.19 2.02 Intr - 10807 10734 74 2 2 49 72 29 0.008 -4.39 2.01 Init - 18518 18284 235 2 1 62 94 231 0.281 19.48 Click here to view a PDF image of the predicted gene(s) Click here for a PostScript image of the predicted gene(s) Predicted peptide sequence(s): >sequence|GENSCAN_predicted_peptide_1|81_aa MRENLELPRDLLKCCNQNGDSNMDNEVQVEEVLDEMRNLLETGAKKHIRQYPIEEHPKLY LTSTPQNSRGHQKQGKSEKLS >sequence|GENSCAN_predicted_peptide_2|170_aa MRQAARGRTWKRKRWSGGVLSSPGRKSQTLPMEASSEPPLDAKSDVSSNLEGEWAARLWS KKDVSLNCVSASVSGHQPVMLKVADHSGQVKTKCFEMTIPQFQNFYRQFKEIAAVIETVA HSCEEPRTAACRSPPVRSDSYQLDELADGPFVHTNYPQTFLLPTLWMPVH Explanation 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). The PROBABILITY of a predicted exon is the estimated probability under GENSCAN's model of genomic sequence structure that the exon is correct. This probability depends in general on global as well as local sequence properties, e.g., it depends on how well the exon fits with neighboring exons. It has been shown that predicted exons with higher probabilities are more likely to be correct than those with lower probabilities.