MicroFootPrinter News

September 21, 2012

  • MicroFootPrinter's database has been updated to include all of Genbank's completed microbial genomes that have RefSeq IDs.

January 29, 2012

  • MicroFootPrinter's database has been updated to include all of Genbank's completed microbial genomes that have RefSeq IDs. The database now contains 2734 replicons.

March 30, 2010

  • MicroFootPrinter's database has been updated to include all of Genbank's 1101 completed microbial genomes (79 archea, 1022 bacteria).

September 15, 2008

  • A filter has been added to discard any extracted cis-regulatory sequences that are nearly identical to another extracted cis-regulatory sequence, in order to avoid undue bias of the motif discovery phase by the presence of several nearly identical sequences. In particular, if two orthologous cis-regulatory regions are at least 90% identical (as determined by pairwise sequence alignment) over at least 70% of the length of the shorter one, one of them will be discarded before FootPrinter is invoked. Even with such sequence elimination, MicroFootPrinter tries to provide as many cis-regulatory sequences as the user requests.

April 1, 2008

  • MicroFootPrinter's database has been updated to include all of Genbank's 668 completed microbial genomes (52 archea, 616 bacteria).

November 1, 2007:

  • MicroFootPrinter's database has been updated to include all of Genbank's 595 completed microbial genomes (47 archea, 548 bacteria). This is nearly twice the number of completed genomes that were available when MicroFootPrinter was launched in 2006.
  • When extracting cis-regulatory regions, MicroFootPrinter now handles all Genbank annotated tRNA and rRNA genes similarly to its handling of protein-coding genes. In particular, the cis-regulatory region that MicroFootPrinter extracts for gene G extends to the shorter of (a) 500 bp upstream of its start codon, or (b) to the nearest upstream protein-coding or RNA gene. However, if a protein-coding or RNA gene appears to be within the same operon as G, rather than terminating
    the cis-regulatory region, the gene will be masked out of the extracted region and replaced with the string NNNNNNNNNN (10 N's for a protein-coding gene) or NNNNNNNN (8 N's for an RNA gene), respectively. See

    for more details about the handling of operons.