![]() |
dan |
% dan Input sequence: embl:paamir Enter window size [20]: Enter Shift Increment [1]: Enter DNA concentration (nM) [50.]: Enter salt concentration (mM) [50.]: Output file [paamir.dan]:An example of producing a plot of Tm:
% dan -plot Input sequence(s): embl:paamir Enter window size [20]: Enter Shift Increment [1]: Enter DNA concentration (nM) [50.]: Enter salt concentration (mM) [50.]: Enter minimum temperature [55.]: Graph type [x11]:
Mandatory qualifiers (* if not always prompted): [-sequence] seqall Sequence database USA -windowsize integer 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. -shiftincrement integer 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. -dnaconc float Enter DNA concentration (nM) -saltconc float Enter salt concentration (mM) * -formamide float This specifies the percent formamide to be used in calculations (it is ignored unless -product is used). * -mismatch float This specifies the percent mismatch to be used in calculations (it is ignored unless -product is used). * -prodlen integer This specifies the product length to be used in calculations (it is ignored unless -product is used). * -mintemp float Enter a minimum value for the temperature scale (y-axis) of the plot. * -graph xygraph Graph type * -outfile report 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. Optional qualifiers (* if not always prompted): * -temperature float If -thermo has been specified then this specifies the temperature at which to calculate the DeltaG, DeltaH and DeltaS values. Advanced qualifiers: -rna boolean This specifies that the sequence is an RNA sequnce and not a DNA sequence. -product boolean This prompts for percent formamide, percent of mismatches allowed and product length. -thermo boolean Output the DeltaG, DeltaH and DeltaS values of the sequence windows to the output data file. -plot boolean 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. General qualifiers: -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-sequence] (Parameter 1) |
Sequence database USA | Readable sequence(s) | Required |
-windowsize | 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 | 20 |
-shiftincrement | 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 | 1 |
-dnaconc | Enter DNA concentration (nM) | Number from 1.000 to 100000.000 | 50. |
-saltconc | Enter salt concentration (mM) | Number from 1.000 to 1000.000 | 50. |
-formamide | This specifies the percent formamide to be used in calculations (it is ignored unless -product is used). | Number from 0.000 to 100.000 | 0. |
-mismatch | This specifies the percent mismatch to be used in calculations (it is ignored unless -product is used). | Number from 0.000 to 100.000 | 0. |
-prodlen | This specifies the product length to be used in calculations (it is ignored unless -product is used). | Any integer value | Window size (20) |
-mintemp | Enter a minimum value for the temperature scale (y-axis) of the plot. | Number from 0.000 to 150.000 | 55. |
-graph | Graph type | EMBOSS has a list of known devices, including postscript, ps, hpgl, hp7470, hp7580, meta, colourps, cps, xwindows, x11, tektronics, tekt, tek4107t, tek, none, null, text, data, xterm, png | EMBOSS_GRAPHICS value, or x11 |
-outfile | 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. | Report file | |
Optional qualifiers | Allowed values | Default | |
-temperature | 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 | 25. |
Advanced qualifiers | Allowed values | Default | |
-rna | This specifies that the sequence is an RNA sequnce and not a DNA sequence. | Yes/No | No |
-product | This prompts for percent formamide, percent of mismatches allowed and product length. | Yes/No | No |
-thermo | Output the DeltaG, DeltaH and DeltaS values of the sequence windows to the output data file. | Yes/No | No |
-plot | 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. | Yes/No | No |
The output is a standard EMBOSS report file.
The results can be output in one of several styles by using the command-line qualifier -rformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: embl, genbank, gff, pir, swiss, trace, listfile, dbmotif, diffseq, excel, feattable, motif, regions, seqtable, simple, srs, table, tagseq
See: http://www.uk.embnet.org/Software/EMBOSS/Themes/ReportFormats.html for further information on report formats.
By default dan writes a 'seqtable' report file.
This is the start and the end of the output file from the example.
######################################## # Program: dan # Rundate: Mon Feb 11 12:07:10 2002 # Report_file: paamir.dan ######################################## #======================================= # # Sequence: PAAMIR from: 1 to: 2167 # HitCount: 2148 #======================================= Start End Tm GC DeltaG DeltaH DeltaS TmProd Sequence 1 20 64.9 70.0 . . . . ggtaccgctggccgagcatc 2 21 63.7 65.0 . . . . gtaccgctggccgagcatct 3 22 63.7 65.0 . . . . taccgctggccgagcatctg 4 23 66.9 70.0 . . . . accgctggccgagcatctgc 5 24 66.7 70.0 . . . . ccgctggccgagcatctgct 6 25 65.5 70.0 . . . . cgctggccgagcatctgctc 7 26 65.5 70.0 . . . . gctggccgagcatctgctcg 8 27 63.7 65.0 . . . . ctggccgagcatctgctcga 9 28 62.9 60.0 . . . . tggccgagcatctgctcgat 10 29 62.6 65.0 . . . . ggccgagcatctgctcgatc 11 30 61.7 60.0 . . . . gccgagcatctgctcgatca 12 31 60.2 60.0 . . . . ccgagcatctgctcgatcac etc. 2143 2162 65.6 70.0 . . . . ggtggccgccaaccagttcc 2144 2163 64.4 65.0 . . . . gtggccgccaaccagttcct 2145 2164 64.1 65.0 . . . . tggccgccaaccagttcctc 2146 2165 65.4 70.0 . . . . ggccgccaaccagttcctcg 2147 2166 64.2 65.0 . . . . gccgccaaccagttcctcga 2148 2167 62.4 65.0 . . . . ccgccaaccagttcctcgag #--------------------------------------- #---------------------------------------
The header information contains details of the program, date and sequence
Subsequent lines contain columns of data for each window into the sequence as it is moved along, giving:
If the qualifier '-product' is used to make the program prompt for percent formamide percent of mismatches allowed and product length, then the output includes the melting temperature of the specified product:
######################################## # Program: dan # Rundate: Mon Feb 11 12:11:25 2002 # Report_file: paamir.dan ######################################## #======================================= # # Sequence: PAAMIR from: 1 to: 2167 # HitCount: 2148 #======================================= Start End Tm GC DeltaG DeltaH DeltaS TmProd Sequence 1 20 64.9 70.0 . . . 54.9 ggtaccgctggccgagcatc 2 21 63.7 65.0 . . . 52.8 gtaccgctggccgagcatct 3 22 63.7 65.0 . . . 52.8 taccgctggccgagcatctg 4 23 66.9 70.0 . . . 54.9 accgctggccgagcatctgc etc.
If the qualifier '-thermo' is gived then the DeltaG, DeltaH and DeltaS of the sequence in the window is also output.
EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by EMBOSS environment variable EMBOSS_DATA.
Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata".
The directories are searched in the following order:
Program name | Description |
---|---|
banana | Bending and curvature plot in B-DNA |
btwisted | Calculates the twisting in a B-DNA sequence |
chaos | Create a chaos game representation plot for a sequence |
compseq | Counts the composition of dimer/trimer/etc words in a sequence |
freak | Residue/base frequency table or plot |
isochore | Plots isochores in large DNA sequences |
wordcount | Counts words of a specified size in a DNA sequence |
This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.uk)