evolve.txt

比对算法的具体应用DNA序列分析 ——基因序列 ——基因表达调控信息 寻找基因牵涉到两个方面的工作 ： 识别与基因相关的特殊序列信号 预测基因的编码区域 结合两个方面的结果确定基因的位置和结构 基因表

***  GENOME EXPLORER HELP FILE  ***

To provide help on using the GUI, and information about how the programs run

Contents

1)  Outline of Function
2)  Parameters loaded from the .inf file (settings menu)
3)  The User Interface
4)  Underlying Method


---  EVOLVE  ---

---  1)  Outline of Function ---

Evolve creates a genome by building each sequence from scratch according to 
user defined criteria.  It then evolves that genome (again according to user 
defined criteria) to produce a phylogeny.

Evolution mirrors biological evolution as far as possible.

 1)  Point Mutations
		   The possibility that a nucleotide may mutate is assessed for every 
		   nucleotide in every sequence on the first chromosome.  If a point 
		   mutation is required it is performed immediately.
 
 2)	 Non-Homologous Recombination event
       The first chromosome is assessed once to see whether it will mutate.  
       Inversion, Deletion and Duplication events occur immediately.  
       Translocation events are delayed until the genome evolves.
	 
 3)  The above two cycles are repeated for every chromosome in the first genome

 4)  Transposon Jumping
       Each chromosome asks each of its transposons if they're active. 
       If a transposon is active, its activity is determined.  
       If the activity involves leaving a footprint the transposon is deleted 
       from the chromosome immediately, and a footprint inserted in its place.  
       If the activity involves a 'jump', a duplicate of the transposon is added 
       to a list of jumping transposons (held by the TransposonJumper object 
       within the genome).  Every transposon in the list of jumping 
       transposons is then randomly inserted into the genome (so could end up 
       anywhere, in any chromosome).

 5)  Translocation
       For every pair of chromosomes flagged for translocation, a translocation 
       event occurs.  In both chromosomes a transposon marker is identified (randomly), 
       and all sequences after the marker are translocated to the other chromosome.  
       A chromosome flagged for translocation will always pair with its 'nearest' 
       flagged chromosome (chromosome with the nearest index in the array of 
       chromosomes held in the genome).

 6)  Polyploidy
      the genome is assessed to determine whether a polyploidy event will occur.  
      If it does, a speciation event also occurs.
 
 7)  Speciation
      the genome is assessed to determine whether speciation will occur 
      (if a polyploidy event is set to occur, speciation will always occur 
      first, and only the original genome will go polyploid).  Speciation 
      involves an identical copy of the genome being created and added to the 
      end of the species array held within the Phylogeny object.
 
 8)  Steps 1-7 are repeated for every species that was in the phylogeny 
      before this generation evolution started (i.e. new species that evolve in 
      step 7 will NOT evolve at all this generation.


---  2)  Parameters loaded from the .inf file (settings menu) ---

evolveOutDir default directory in which to write an NEW directory (based on date
             and time) in which all phylogenies created in this program run will be 
             written

---  3)  The User Interface  ---

number of phylogenies to generate
     the number of phylogenies to generate using this criteria.  A new 'seed' genome
     will be created for each phylogeny produced.

output a homology file (and no fasta files)
     To be used when sequence evolution is prevented.  Outputs a homology file that
     can be converted to a gene-order matrix (with or without interference added - 
     see "gene order matrix from homol file" documentation.

include transposons
     Includes transposons in the homology file.
     
assume all transposon homologous
     Assigns all transposons the same homolId in the homology file.

output a gene order file
     Generates a gene-order file from the homology file (with NO interference).

output geneOrders for all combinations
     Outputs homology or gene order files for all the options in the drop down 
     list below.

construct homology from
     Uses the selected species to construct the homology.
       Only Evolved Species: all "extant" species - includes the outgroup.
       Evolved Species and Original Ancestor: includes the outgroup and the original 
                             ancestor from which the entire phylogeny was generated.
       Evolved Species and All Ancestors: includes the outgroup, and all ancestral
                             species (species at the nodes of the tree).
       Only Ancestors: produces a gene-order file for the ancestors (species at nodes
                             of the tree) only.

EVOLVE TAB


allow all types of evolution 
prevent sequence evolution 
prevent chromosome evolution
     radio buttons to indicate how evolution may proceed.  If no sequence evolution is
     required the program runs far more efficiently if the 'prevent sequence evolution'
     button is selected, than if all sequence evolution parameters are set to zero.

number of generations
     the number of generation over which to evolve a phylogeny

minimum number of species
     the minimum number of species in the finished phylogeny.  If the desired number of
     generations have been run, but this number has not been reached, the phylogeny will
     continue to evolve until the required number of species are present.

maximum number of species
     if this value is set it prevents speciation from occurring once the designated
     number of species has been reached.  Set min and max number of species to identical
     values to force phylogenies of a particular number of species.

min number of generations after last speciation event
     this will force a further set of generations, even if number of generations has been
     reached before this speciation event.  BEWARE!  Don't set this value if you have a 
     high speciation coefficient because the program may end up running forever!

save genomes in
     a new directory (based on date and time) will be created within this directory.
     all phylogenies will then be written to the date_time directory.

fasta line length
     the number of residues on a single line of fasta output


CHROMOSOME TAB

non-homologous recombination ratio
     enter the percentage of non-homologous recombinations that are inversions, deletions,
     duplications and translocations.  These values MUST add up to 100%.

small event coefficient (percentage)
     the percent of non-homologous recombinations that are small events (involve less than
     or equal to the number of sequences in 'largest small event segment size' field).
     A random number generator uses this coefficient to decide whether an event will be 
     small or large (bigger than 'largest small event segment size').  It will then force
     the event to be small (or large) IF the chromosome can meet these criteria.  If the
     chromosome has only two transposons and they're 12 sequences apart, it cannot be 
     forced to undergo an event involving 5 sequences or fewer.  In these cases the event
     will default to whatever size is possible. Set this and 'largest small event segment
     size' to zero to disable this function.

largest small event segment size (not counting flanking transposons)
     the largest number of sequences between two flanking transposons that will qualify as a 
     'small event'.  Set this and 'small event coefficient' to zero to disable this function.

number of sequences per initial chromosome
     the number of sequences per chromosome when the 'seed' genome is created

number of chromosomes in original species
     the number of chromosomes in the 'seed' genome

non-homologous-recombination-coefficient (percentage)
     the percent chance that a chromosome will 'fail to align correctly' and mutate during
     replication.  'Failure to align' ALWAYS results in an event UNLESS the selected event
     required two transposons and the chromosome involved has only one or none at all.

polyploidy coefficient (percent)
     the percent chance of a polyploidy (genome duplication within this species) event 
     occurring during replication.  
     (polyploidy events are ALWAYS followed by speciation events)

speciation coefficient (percent)
     the percent chance of replication being immediately followed by speciation.
     speciation is simulated by an exact copy of this genome being added to the 
     genomes currently held within the phylogeny


SEQUENCE TAB


percent of new sequences that are
     sets the percent of sequences in the 'seed' genome that are genes, transposons, 
     footprints or introns - MUST add to 100%
     Transposons are REQUIRED for chromosome mutation.  When a transposon jumps, it
     may leave a footprint (depending of user settings).
		 
sequence length ratio
     The percent of sequences of each type in the 'seed' genome, being of a particular
     length.  In each table the values must MUST add to 100%


TRANSPOSON TAB


transposon activity ratio
     percent chance that an active transposon will 
       a) jump and leave replicate
       b) delete itself and leave a footprint
       c) jump and leave a footprint
     Values MUST add to 100%

transposon activity coefficient
     percent chance that a transposon will be active during each genome replication.
     The left hand column is the 'percent of transposons' as they are added to the 
     'seed' genome.  This column MUST add to 100%
     The right hand column is the percent chance that the transposon will be active
     during replication.


POINT MUTATION TAB


point mutation ratio
     percent chance that when a point mutation occurs it will be a transition,
     transversion, insertion, or deletion.  
     Values MUST add to 100%

point mutation coefficient
     percent chance that a nucleotide will mutate during replication
     The left hand column is the percent of nucleotides in the original 'seed' genome
     with the corresponding chance of mutation. Values in the left hand column
     MUST add to 100%.



---  4)  Underlying Method   ---


see explanation in 'outline of function' section