dan.txt

emboss的linux版本的源代码

                                    dan 



Function

   Calculates DNA RNA/DNA melting temperature

Description

   Dan calculates the melting temperature (Tm) and the percent G+C of a
   nucleic acid sequence (optionally plotting them). For the Melting
   temperature profile, free energy values calculated from nearest
   neighbor thermodynamics are used (Breslauer et al. Proc. Natl. Acad.
   Sci. USA 83, 3746-3750 and Baldino et al. Methods in Enzymol. 168,
   761-777).

Usage

   Here is a sample session with dan


% dan 
Calculates DNA RNA/DNA melting temperature
Input nucleotide sequence(s): tembl:paamir
Enter window size [20]: 
Enter Shift Increment [1]: 
Enter DNA concentration (nM) [50.]: 
Enter salt concentration (mM) [50.]: 
Output report [paamir.dan]: 

   Go to the input files for this example
   Go to the output files for this example

   Example 2

   An example of producing a plot of Tm:


% dan -plot -graph cps 
Calculates DNA RNA/DNA melting temperature
Input nucleotide sequence(s): tembl:paamir
Enter window size [20]: 
Enter Shift Increment [1]: 
Enter DNA concentration (nM) [50.]: 
Enter salt concentration (mM) [50.]: 
Enter minimum temperature [55.]: 

Created dan.ps

   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers (* if not always prompted):
  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
                                  format, or reference (input USA)
   -windowsize         integer    [20] The values of melting point and other
                                  thermodynamic properties of the sequence are
                                  determined by taking a short length of
                                  sequence known as a window and determining
                                  the properties of the sequence in that
                                  window. The window is incrementally moved
                                  along the sequence with the properties being
                                  calculated at each new position. (Integer
                                  from 1 to 100)
   -shiftincrement     integer    [1] This is the amount by which the window
                                  is moved at each increment in order to find
                                  the melting point and other properties along
                                  the sequence. (Integer 1 or more)
   -dnaconc            float      [50.] Enter DNA concentration (nM) (Number
                                  from 1.000 to 100000.000)
   -saltconc           float      [50.] Enter salt concentration (mM) (Number
                                  from 1.000 to 1000.000)
*  -mintemp            float      [55.] Enter a minimum value for the
                                  temperature scale (y-axis) of the plot.
                                  (Number from 0.000 to 150.000)
*  -graph              xygraph    [$EMBOSS_GRAPHICS value, or x11] Graph type
                                  (ps, hpgl, hp7470, hp7580, meta, cps, x11,
                                  tekt, tek, none, data, xterm, png)
*  -outfile            report     [*.dan] If a plot is not being produced then
                                  data on the melting point etc. in each
                                  window along the sequence is output to the
                                  file.

   Additional (Optional) qualifiers (* if not always prompted):
   -product            toggle     This prompts for percent formamide, percent
                                  of mismatches allowed and product length.
*  -formamide          float      [0.] This specifies the percent formamide to
                                  be used in calculations (it is ignored
                                  unless -product is used). (Number from 0.000
                                  to 100.000)
*  -mismatch           float      [0.] This specifies the percent mismatch to
                                  be used in calculations (it is ignored
                                  unless -product is used). (Number from 0.000
                                  to 100.000)
*  -prodlen            integer    [Window size (20)] This specifies the
                                  product length to be used in calculations
                                  (it is ignored unless -product is used).
                                  (Any integer value)
   -thermo             toggle     Output the DeltaG, DeltaH and DeltaS values
                                  of the sequence windows to the output data
                                  file.
*  -temperature        float      [25.] If -thermo has been specified then
                                  this specifies the temperature at which to
                                  calculate the DeltaG, DeltaH and DeltaS
                                  values. (Number from 0.000 to 100.000)

   Advanced (Unprompted) qualifiers:
   -rna                boolean    This specifies that the sequence is an RNA
                                  sequence and not a DNA sequence.
   -plot               toggle     If this is not specified then the file of
                                  output data is produced, else a plot of the
                                  melting point along the sequence is
                                  produced.

   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

   "-graph" associated qualifiers
   -gprompt            boolean    Graph prompting
   -gdesc              string     Graph description
   -gtitle             string     Graph title
   -gsubtitle          string     Graph subtitle
   -gxtitle            string     Graph x axis title
   -gytitle            string     Graph y axis title
   -goutfile           string     Output file for non interactive displays
   -gdirectory         string     Output directory

   "-outfile" associated qualifiers
   -rformat            string     Report format
   -rname              string     Base file name
   -rextension         string     File name extension
   -rdirectory         string     Output directory
   -raccshow           boolean    Show accession number in the report
   -rdesshow           boolean    Show description in the report
   -rscoreshow         boolean    Show the score in the report
   -rusashow           boolean    Show the full USA in the report
   -rmaxall            integer    Maximum total hits to report
   -rmaxseq            integer    Maximum hits to report for one sequence

   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

Input file format

   Any DNA or RNA sequence USA.

  Input files for usage example

   'tembl:paamir' is a sequence entry in the example nucleic acid
   database 'tembl'

  Database entry: tembl:paamir

ID   PAAMIR     standard; DNA; PRO; 2167 BP.
XX
AC   X13776; M43175;
XX
SV   X13776.1
XX
DT   19-APR-1989 (Rel. 19, Created)
DT   17-FEB-1997 (Rel. 50, Last updated, Version 22)
XX
DE   Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation
XX
KW   aliphatic amidase regulator; amiC gene; amiR gene.
XX
OS   Pseudomonas aeruginosa
OC   Bacteria; Proteobacteria; gamma subdivision; Pseudomonadaceae; Pseudomonas
.
XX
RN   [1]
RP   1167-2167
RA   Rice P.M.;
RT   ;
RL   Submitted (16-DEC-1988) to the EMBL/GenBank/DDBJ databases.
RL   Rice P.M., EMBL, Postfach 10-2209, Meyerhofstrasse 1, 6900 Heidelberg, FRG
.
XX
RN   [2]
RP   1167-2167
RX   MEDLINE; 89211409.
RA   Lowe N., Rice P.M., Drew R.E.;
RT   "Nucleotide sequence of the aliphatic amidase regulator gene of Pseudomona
s
RT   aeruginosa";
RL   FEBS Lett. 246:39-43(1989).
XX
RN   [3]
RP   1-1292
RX   MEDLINE; 91317707.
RA   Wilson S., Drew R.;
RT   "Cloning and DNA seqence of amiC, a new gene regulating expression of the
RT   Pseudomonas aeruginosa aliphatic amidase, and purification of the amiC
RT   product.";
RL   J. Bacteriol. 173:4914-4921(1991).
XX
RN   [4]
RP   1-2167
RA   Rice P.M.;
RT   ;
RL   Submitted (04-SEP-1991) to the EMBL/GenBank/DDBJ databases.
RL   Rice P.M., EMBL, Postfach 10-2209, Meyerhofstrasse 1, 6900 Heidelberg, FRG
.
XX
DR   SWISS-PROT; P10932; AMIR_PSEAE.
DR   SWISS-PROT; P27017; AMIC_PSEAE.
DR   SWISS-PROT; Q51417; AMIS_PSEAE.


  [Part of this file has been deleted for brevity]

FT                   phenotype"
FT                   /replace=""
FT                   /gene="amiC"
FT   misc_feature    1
FT                   /note="last base of an XhoI site"
FT   misc_feature    648..653
FT                   /note="end of 658bp XhoI fragment, deletion in  pSW3 cause
s
FT                   constitutive expression of amiE"
FT   conflict        1281
FT                   /replace="g"
FT                   /citation=[3]
XX
SQ   Sequence 2167 BP; 363 A; 712 C; 730 G; 362 T; 0 other;
     ggtaccgctg gccgagcatc tgctcgatca ccaccagccg ggcgacggga actgcacgat        6
0
     ctacctggcg agcctggagc acgagcgggt tcgcttcgta cggcgctgag cgacagtcac       12
0
     aggagaggaa acggatggga tcgcaccagg agcggccgct gatcggcctg ctgttctccg       18
0
     aaaccggcgt caccgccgat atcgagcgct cgcacgcgta tggcgcattg ctcgcggtcg       24
0
     agcaactgaa ccgcgagggc ggcgtcggcg gtcgcccgat cgaaacgctg tcccaggacc       30
0
     ccggcggcga cccggaccgc tatcggctgt gcgccgagga cttcattcgc aaccgggggg       36
0
     tacggttcct cgtgggctgc tacatgtcgc acacgcgcaa ggcggtgatg ccggtggtcg       42
0
     agcgcgccga cgcgctgctc tgctacccga ccccctacga gggcttcgag tattcgccga       48
0
     acatcgtcta cggcggtccg gcgccgaacc agaacagtgc gccgctggcg gcgtacctga       54
0
     ttcgccacta cggcgagcgg gtggtgttca tcggctcgga ctacatctat ccgcgggaaa       60
0
     gcaaccatgt gatgcgccac ctgtatcgcc agcacggcgg cacggtgctc gaggaaatct       66
0
     acattccgct gtatccctcc gacgacgact tgcagcgcgc cgtcgagcgc atctaccagg       72
0
     cgcgcgccga cgtggtcttc tccaccgtgg tgggcaccgg caccgccgag ctgtatcgcg       78
0
     ccatcgcccg tcgctacggc gacggcaggc ggccgccgat cgccagcctg accaccagcg       84
0