BPROM -New Recognition of E.coli promoter and start of transcription program

Victor softberry at softberry.com
Mon Jan 20 05:44:36 EST 2003


BPROM - Recognition of E.coli promoter and start of transcription

 As part of Bacterial genome analysis suit of programs and enforce
operon and gene prediction by FgenesB program we develop BPROM program
to predict bacterial promoters

  Program available on line at

http://www.softberry.com/berry.phtml?topic=gfindb

http://www.softberry.com/berry.phtml?topic=promoter

Method description:

Algorithm predicts potential transcription start positions of bacterial
genes
regulated by sigma70 promoters (major E.coli promoter class). linear
discriminant
function (LDF) combining characteristics describing functional motifs and
oligonucleotide
composition of these sites. BPROM has accuracy of E.coli promoter
recognition ~80%.
Its specificity ~80 when tested on equal size sets of promoter and
non-promoter sequences.
It is not advisable to run it on the whole genomes. To avoid many false
positive prediction
run BPROM on the region between 2 neighbor ORF (in one ORF frame) or on ORF
upstream
sequence having in mind that most promoters is localized within 150 bases
before the
start of corresponding coding region.

BPROM output:
First line - name of your sequence;
Second and Third lines - LDF threshold and the length of presented sequence
4th line - The number of predicted promoters
Next lines - positions of predicted promoters, and their scores with
'weights' of two
conserved promoter boxes. Promoter position assign to the first nucleotide
of the
transcript (Transcription Start Site position).
After that we present elements of Transcriptional factor binding sites for
each
predicted promoter (if they found).

For example:
bprom  Sat Jan 18 21:11:25 EST 2003
>Region of E.coli genome between protein_id="AAC76687.1" and
protein_id="AAC7668
 Length of sequence-       420
 Threshold for promoters -  0.20
 Number of predicted promoters -      1
 Promoter Pos:    145 LDF-  6.02
 -10 box at pos.    130 ctttatgat Score    66
 -35 box at pos.    109 tttaat    Score    36

 Oligonucleotides from known TF binding sites:

 For promoter at    145:
        fis:  TCTTTAAT at position     107 Score -   6
     rpoD17:  TTATGATA at position     132 Score -   7
       lexA:  ATAAATAA at position     137 Score -  14
     rpoD17:  ATAATAAT at position     141 Score -   8


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