emma.ihelp

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                                  used. INCREASE for speed (max= 2 for
                                  proteins; 4 for DNA), DECREASE for
                                  sensitivity. For longer sequences (e.g.
                                  >1000 residues) you may need to increase the
                                  default. (integer from 0 to 4)
*  -gapw               integer    [3 for protein, 5 for nucleic] This is a
                                  penalty for each gap in the fast alignments.
                                  It has little affect on the speed or
                                  sensitivity except for extreme values.
                                  (Positive integer)
*  -topdiags           integer    [5 for protein, 4 for nucleic] The number of
                                  k-tuple matches on each diagonal (in an
                                  imaginary dot-matrix plot) is calculated.
                                  Only the best ones (with most matches) are
                                  used in the alignment. This parameter
                                  specifies how many. Decrease for speed;
                                  increase for sensitivity. (Positive integer)
*  -window             integer    [5 for protein, 4 for nucleic] This is the
                                  number of diagonals around each of the
                                  'best' diagonals that will be used. Decrease
                                  for speed; increase for sensitivity.
                                  (Positive integer)
*  -nopercent          boolean    [N] Fast pairwise alignment: similarity
                                  scores: suppresses percentage score
   -gapopen            float      [10.0] The penalty for opening a gap in the
                                  alignment. Increasing the gap opening
                                  penalty will make gaps less frequent.
                                  (Positive foating point number)
   -gapextend          float      [5.0] The penalty for extending a gap by 1
                                  residue. Increasing the gap extension
                                  penalty will make gaps shorter. Terminal
                                  gaps are not penalised. (Positive foating
                                  point number)
   -[no]endgaps        boolean    [Y] End gap separation: treats end gaps just
                                  like internal gaps for the purposes of
                                  avoiding gaps that are too close (set by
                                  'gap separation distance'). If you turn this
                                  off, end gaps will be ignored for this
                                  purpose. This is useful when you wish to
                                  align fragments where the end gaps are not
                                  biologically meaningful.
   -gapdist            integer    [8] Gap separation distance: tries to
                                  decrease the chances of gaps being too close
                                  to each other. Gaps that are less than this
                                  distance apart are penalised more than
                                  other gaps. This does not prevent close
                                  gaps; it makes them less frequent, promoting
                                  a block-like appearance of the alignment.
                                  (Positive integer)
*  -norgap             boolean    [N] Residue specific penalties: amino acid
                                  specific gap penalties that reduce or
                                  increase the gap opening penalties at each
                                  position in the alignment or sequence. As an
                                  example, positions that are rich in glycine
                                  are more likely to have an adjacent gap
                                  than positions that are rich in valine.
*  -hgapres            string     [GPSNDQEKR] This is a set of the residues
                                  'considered' to be hydrophilic. It is used
                                  when introducing Hydrophilic gap penalties.
                                  (Any string is accepted)
*  -nohgap             boolean    [N] Hydrophilic gap penalties: used to
                                  increase the chances of a gap within a run
                                  (5 or more residues) of hydrophilic amino
                                  acids; these are likely to be loop or random
                                  coil regions where gaps are more common.
                                  The residues that are 'considered' to be
                                  hydrophilic are set by '-hgapres'.
   -maxdiv             integer    [30] This switch, delays the alignment of
                                  the most distantly related sequences until
                                  after the most closely related sequences
                                  have been aligned. The setting shows the
                                  percent identity level required to delay the
                                  addition of a sequence; sequences that are
                                  less identical than this level to any other
                                  sequences will be aligned later. (Integer
                                  from 0 to 100)

   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -sformat1           string     Input sequence format
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-outseq" associated qualifiers
   -osformat2          string     Output seq format
   -osextension2       string     File name extension
   -osname2            string     Base file name
   -osdirectory2       string     Output directory
   -osdbname2          string     Database name to add
   -ossingle2          boolean    Separate file for each entry
   -oufo2              string     UFO features
   -offormat2          string     Features format
   -ofname2            string     Features file name
   -ofdirectory2       string     Output directory

   "-dendoutfile" associated qualifiers
   -odirectory3        string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages