Genes/Operons in pathogenic organisms:

Victor Solovyev softberry at softberry.com
Tue Nov 19 15:32:37 EST 2002


Genes/Operons in pathogenic organisms: Mycobacterium
tuberculosis, Yersinia
pestis and others

Applying Softberry fgenesB-annotator script that
predicts genes and find
similar
proteins in public databases, we present annotations
for several pathogenic
organisms
 at:
 
 

http://www.softberry.com/berry.phtml?topic=fgenesb_ann
 
Mycobacterium tuberculosis H37Rv, complete genome
 Mycobacterium tuberculosis CDC1551, complete genome
 Yersinia pestis strain CO92, complete genome
 Yersinia pestis KIM, complete genome
 Bacillus anthracis A2012 main chromosome
 
  Example of annotation of Yersinia pestis KIM
 
 Prediction of potential operons and genes in
 microbial  genomes
  Time:   Mon Nov 18 11:07:36 2002
  Seq name: gi|22123922|ref|NC_004088.1| Yersinia
 pestis KIM, complete genome
  Length of sequence - 4600755 bp
  Number of predicted genes - 4011, with homology -
 3927
  Number of transcription units - 2364, operons – 799
 
 N      Tu/Op   Conserved  S             Start       
  End    Score
                 pairs(N/Pv)
 1     1 Op  1   2/0.311   -    CDS         21 -     
  461    375  ## COG0716
 Flavodoxins
 2     1 Op  2     .       -    CDS        554 -     
 1015    362  ## COG1522
 Transcriptional regulators
 3     2 Tu  1     .       +    CDS       1185 -     
 2177   1148  ## COG2502
 Asparagine synthetase A
 … … … … … … … … … … … … … … … … … … … … … … … … … …
 … … … … … …
 
 New FgenesB is the fastest (E.coli genome analyzed
 in ~14 sec) and most
 accurate ab initio Bacterial gene prediction program
 available.
 
 	http://www.softberry.com/berry.phtml?topic=fgenesb
 
 It uses parameters learned for different bacteria by
 FgenesB-train script,
 which input is just new bacterial sequence. It will
 automatically create
 file with gene prediction parameters for the
 analyzed organism.
 It takes only ~10 minutes to create such file for
 such genome as
 E.coli using its sequence. If you need parameters
 for your new bacteria,
 please contact Softberry Inc., we can include them
 in the WEB list.
 
 
 Algorithm based on pattern recognition of different
 types of signals
 and Markov chain models of coding regions. Optimal
 combination of these
 features is then found by dynamic programming and a
 set of gene models
 is constructed along given sequences.
 
 
 In the current FgenesB version  operon prediction
 model is realized
 based on gene distances. It can recognize accurately
 70% of single
 transcription units and define exactly about 43% of
 operons (~92%
 partially).
 
 --- 

=====



Moderated
bionet.genome.gene-structure



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