MicroFootPrinter Q&A










	Clade?
	A method to restrict species used by the program to a specified subtree of the phylogeny. The default (All) has no such restriction. A number shown in parentheses next to a clade indicates how many replicons (chromosomes plus plasmids) in the database belong to it. A larger number gives more opportunity to find up to the specified maximum number of species for comparison.









	FootPrinter?
	The part of MicroFootPrinter (this program) responsible for finding evolutionarily conserved nucleotide sequences, or motifs, in DNA Regulatory Regions, and for creating the final visual output.


	FootPrinter can be run directly by visiting here. One advantage to using the standalone FootPrinter program is greater flexibility in input parameter selections. Another is that it is not constrained to microbial genomes. You may use the Regulatory Regions and Phylogeny outputs from this program as inputs to FootPrinter.









	Maximum number of mutations?
	The maximum parsimony score allowed for reported motifs. The parsimony score is the number of nucleotide substitutions along branches of the phylogenetic (evolutionary) tree necessary to explain all the differences among the motif instances.









	Maximum number of species?
	The maximum (and target) number of species used for comparison by FootPrinter, including the species of interest.









	MicroFootPrinter (MFP)?
	This program - brought to you from the University of Washington's Computational Biology group. MicroFootPrinter is a front end to the FootPrinter program, with specific focus on microbial genomes. Much of the purpose of MicroFootPrinter is to attempt to automatically optimize the most difficult input parameter selections to FootPrinter.









	Motif?
	A collection of instances each of which is similar to all others as constrained by a number of factors including the maximum number of mutations allowed, the motif size specified, and the phylogenetic relationship between the species chosen by the program.









	Motif instance?
	An identified sequence of consecutive nucleotides. The number of nucleotides in any instance is set by the value selected for motif size. An instance belongs to a group of instances that together make up a motif.









	Motif size?
	The exact number of consecutive nucleotides that must make up each instance of a motif.









	Target number of motifs?
	The number of motifs you would like to see in the final output display of the program. If the program is not acheiving your target number, you can try any one or combination of: Reduce the motif size sought Increase the maximum number of species Increase the maximum number of mutations Choose a larger clade to select species from You may instead receive a few more than your target number. In this case, it means that some motifs are strict subsets of others in terms of their constituent instances . Such items are not counted more than once when trying to achieve the target number.