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TSSW - Recognition of human PolII promoter region and start of transcriptionMethod description:Algorithm predicts potential transcription start positions by linear discriminant function combining characteristics describing functional motifs and oligonucleotide composition of these sites. TSSW uses file with selected factor binding sites from currently supported functional site data base of (E.Wingender, J.of Biotechnology,1994, 35, 273-280). For approximately 50-55% level of true promoter region recognition, TSSW program will give one false positive prediction for about 4000 bp. Another promoter recognition program, TSSG, uses promoter.dat file with selected factor binding sites (TFD, Ghosh,1993). References: TSSW output example:HSCALCAC 7637 bp DNA PRI 14-MAR-1995 Length of sequence- 7637 Threshold for LDF- 4.00 2 promoter(s) were predicted Pos.: 1834 LDF- 11.08 TATA box predicted at 1804 Pos.: 7031 LDF- 4.64 TATA box predicted at 7001 Transcription factor binding sites: for promoter at position - 1834 1752 (+) CHICK$ACRA CCGCCC 1762 (-) HS$BAC_03 CCAAT 1764 (-) RAT$ALBU_2 AACCAAT 1757 (-) HS$APOE_08 GGGCGG 1575 (+) HS$ACHGON_ TGACGTCA 1582 (-) HS$ACHGON_ TGACGTCA 1758 (+) MOUSE$A21C ATTGG 1745 (+) MOUSE$A21C gcccagccctcccATTGGtggagacg 1609 (+) Y$CYC1_09 ctcatttggcgagcGTTGGt 1724 (+) AD$E2L_04 TGACgcA 1577 (+) AD$E4_16 ACGTCA 1580 (-) AD$E4_16 ACGTCA 1580 (-) AD$E4_18 ACGTCAT 1655 (+) HS$EGFR_15 TCAAT .............................. Where:
First line - name of your sequence;
Lower cased letters mean non-conserved nucleotides in the site consensus The letters except (A,T,G,C) describe ambiguous sites in a given DNA sequence motif, where a single character may represent more than one nucleotide using Standard IUPAC Nucleotide code. See TABLE at http://www.yeastract.com/help/help_searchbydnamotif.php#Ref1
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