makenucseq

 

Function

Creates random nucleotide sequences

Description

Makes a set of random sequences. The sequence composition can be defined by reading an optional codon usage file.

Algorithm

**************** EDIT HERE ****************

Usage

Here is a sample session with makenucseq


% makenucseq 
Creates random nucleotide sequences
Codon usage file (optional): 
Number of sequences created [100]: 
Length of each sequence [100]: 
nucleotide output sequence(s) [makeseq.fasta]: 

Go to the output files for this example

Example 2

Providing a codon usage file specifies the sequence composition. This Pseudomonas aeruginosa file specifies a high GC content.


% makenucseq 
Creates random nucleotide sequences
Codon usage file (optional): Epseae.cut
Number of sequences created [100]: 
Length of each sequence [100]: 
nucleotide output sequence(s) [makeseq.fasta]: 

Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers (* if not always prompted):
   -codonfile          codon      Optional codon usage file. Nucleotide
                                  sequences will be created as triplets
                                  matching the frequencies in the file, with
                                  the end trimmed to be in the correct reading
                                  frame.
   -amount             integer    [100] Number of sequences created (Integer 1
                                  or more)
   -length             integer    [100] Length of each sequence (Integer 1 or
                                  more)
*  -insert             string     String that is inserted into sequence (Any
                                  string is accepted)
*  -start              integer    [1] Start point of inserted sequence
                                  (Integer 1 or more)
  [-outseq]            seqoutall  [.] Nucleotide sequence
                                  set(s) filename and optional format (output
                                  USA)

   Additional (Optional) qualifiers:
   -useinsert          toggle     [N] Do you want to make an insert

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

   "-codonfile" associated qualifiers
   -format             string     Data format

   "-outseq" associated qualifiers
   -osformat1          string     Output seq format
   -osextension1       string     File name extension
   -osname1            string     Base file name
   -osdirectory1       string     Output directory
   -osdbname1          string     Database name to add
   -ossingle1          boolean    Separate file for each entry
   -oufo1              string     UFO features
   -offormat1          string     Features format
   -ofname1            string     Features file name
   -ofdirectory1       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

Standard (Mandatory) qualifiers Allowed values Default
-codonfile Optional codon usage file. Nucleotide sequences will be created as triplets matching the frequencies in the file, with the end trimmed to be in the correct reading frame. Codon usage file in EMBOSS data path  
-amount Number of sequences created Integer 1 or more 100
-length Length of each sequence Integer 1 or more 100
-insert String that is inserted into sequence Any string is accepted An empty string is accepted
-start Start point of inserted sequence Integer 1 or more 1
[-outseq]
(Parameter 1)
Nucleotide sequence set(s) filename and optional format (output USA) Writeable sequence(s)  
Additional (Optional) qualifiers Allowed values Default
-useinsert Do you want to make an insert Toggle value Yes/No No
Advanced (Unprompted) qualifiers Allowed values Default
(none)

Input file format

makenucseq reads any normal sequence USAs.

Output file format

makenucseq outputs a graph to the specified graphics device. outputs a report format file. The default format is ...

Output files for usage example

File: makeseq.fasta

>EMBOSS_001
ggtccgaggggtagcttgatcgcctcttttgggaacgcaagcgtggccggtatgataaaa
taaaatgcgctccgctctggtaagacggacggtcgcccta
>EMBOSS_002
tttcaatccattaggagatccttccgggcttactcttttttggtaggaatacagacgaat
gtgttgttgacactacaagtacgaactgtgatcgcaccct
>EMBOSS_003
aacggctgttagaccgcatcattttggcaggaaccttgggtcggttcatctcttgggtat
gacagcacagggaggtttgagagctgcctcccggattttg
>EMBOSS_004
atcgaagagacgcattcctatagtatcaatccttgacgtcggcatggttcggatcttacg
cgaagccctacgactccctaccggtattgtatcgttctag
>EMBOSS_005
agagttcgtctacacatgggcacccttactacttgagtgcttaccaaaagtacgatccac
gaaacgtcgagcactggcatgcacacgctctccgacgtat
>EMBOSS_006
caatcctcattgcttacacggccacaacaggaagtgcctcaagctgtagagcataggcat
gttctcaagatcgcgttaacagccattgctggagaatggc
>EMBOSS_007
actcggagttcaaccgccgctgtgggctgagctatccctaatgacccgcgcgtagagtgt
taaaatctttcgacagtcacctgcacatcgttgtcttctg
>EMBOSS_008
cgagggtcattctaaatttgagggtaatgctcgcgccatgcgacttgtcgggaaagcggc
cctttatgcgttgccggtcggcattgcccaaccctagtga
>EMBOSS_009
gttatcacgtccaattaggtgggccacaatacgtcggcagaatcaagtgcataacggaga
ggtcactaggacgttactgtcattccctgccccgctatgt
>EMBOSS_010
tatgtttctcgtgctcagcttagaccggagagctccacccaataggccgcacacaagggg
tctttaggatacccccccccttattaccccacagcaacag
>EMBOSS_011
agacgcgccgctcgtagtatgttacctcccttacctgaggacctgcgtggatggcggcaa
cgtgcctcaaagcccgcagcgaatggaaagcaggttggtg
>EMBOSS_012
accctcgcgctgtcgtgtatatttctagcgatgagctagttcgtgcggccatggttctgg
atgcatggctatggtttgttcagacggaatagtccgggac
>EMBOSS_013
accctgacagctcttaccctctatggacggacagggcatgaccgtgcatgacctggcaga
gaacggcttcatattagggagcagcagaatcgtgtatcgt
>EMBOSS_014
tcctgccgggaattagagacaaaaagattgtgaccttcacagcctcctactttcttttgt
tagtatggggcttgacactatacactgggacaatttagaa
>EMBOSS_015
ccgtagcaaggccacagttacgaaggtcatgttcccacccacagcgttgttcccttttac
cgacccacgcctagaatttctcgaagaacagaaaccaccc
>EMBOSS_016
cttctcccgtaagaaccttcgtccaacatccaatcaatcacggtgggtacgaggtatacc
tatctgtcacgaaatcctaagacatttctgcaaacagggg
>EMBOSS_017
cagtagttgatgcacgtaacatttactcattggacaacagcacagtagctcccatcacat


  [Part of this file has been deleted for brevity]

>EMBOSS_084
ttaccatttaaacatgtccagatacggacaggtcgcactgtccttgggccacttttctgt
tacgcgcgtgagcttatgatgacgaatcgcgggaagggat
>EMBOSS_085
cctcactctctcagaccccgaatcctaagtgatcaatacctctacgtcttggttttgccg
ctgatatcatgatatacatgagtctagcacggtctcctac
>EMBOSS_086
aggcagggtatagtgctctagagtacaccccttgcgtgaaatcggcgtcctggtggtcga
ttaccctcaagcacttttcctcagttcggggggtcacgat
>EMBOSS_087
ataagtctaccaatgaaacgatcgcgaatcggacgccactcgccagggtattcgcgcttc
acattatatatagtccggaagcacgactctccatttggtt
>EMBOSS_088
tctatccgtgcctcccacgggtcagatatatgctctggacgtagtggtgccgcatctgtg
tacatgactaaagctacgactttttcgcgtagccaatcca
>EMBOSS_089
ccgccgtaactttcccgggtagggggctaccgacgataatctagcgtttgatagcgtctg
gcgcatgtgtcatagggtgctggtgtccttgggcagtaca
>EMBOSS_090
acgaatccccctttccacacgacaaaaacgagaccggtagctttgggcgagacgtacgct
gactaagcaatcgaagcccttcaagtacgctgccagtcaa
>EMBOSS_091
gtgacctgagacttgagctactaatgcacttgtacgagggcttacaaaaagaacggatca
aagcaagccctcgggatgtgtgacccaggcgtttgccgtg
>EMBOSS_092
accgttcgagagatctcacaactagcacatatacgccagaggtagtcacacagattaaga
tggtgcgacagctcgcgcaaccacacggggatgacacgta
>EMBOSS_093
aaccctaaccgagggtttgtggctaacatcagccccactgtgcccgcaacgtcccaaatt
gactctatctcgttccaacactttaaatgcttatgtatat
>EMBOSS_094
gtctggtacgttcagcgcgattagccgggcgctccggaccggatgtcctaccaggtacac
ctatccagtaccacggcgcggtgtagccgtacctcaaagc
>EMBOSS_095
taggttggatagacgacggtctgtcaaggctcaccaagggttaatctgcctctgataagt
gttggactatgggggcaacgcctcgaccagttgaacctgt
>EMBOSS_096
gaccgtggtgcattctagtacgtatgagcatccaaacatgcgccacatgtaccagggtga
tgctggagtcgctgtggaacaagagcgttctaccccctcg
>EMBOSS_097
atcataggcccaagtcggatcatgtttatccgagtttaacaagttctgcagtggcagaaa
agtgtctttttagcagctcccctattgccacggctgctac
>EMBOSS_098
taactagcagtttcgttatttaagagacttatgcgttaataaaatcttgttatggggcca
ccagtccttattaatccgtaaggagacgagccgcctggag
>EMBOSS_099
tcgggatgggaactgtagtaagtaaatacagcagaacaagaccagctgtaggaccgcaag
taattcgcatggggccttgctctctacaatcacggcagcc
>EMBOSS_100
taaatcggcatggtggagttatctttaagattgcaccatatgtggccgagccggaaaagc
ttatggggtgccaggtttagcctcttgttacatagtgacg

Output files for usage example 2

File: makeseq.fasta

>EMBOSS_001
gggcgtctgggcgccgtcacggtcggccgctacctcgacccggcgttctccgtcaacttc
gcgcggcagggcttcatctgactgctgttcggcgtgcgcgaa
>EMBOSS_002
gacgccggcgcgaccgagcggcaccgcttcgtccgaggaggcggcggcttcaccctcgtg
gccttcgacgacagcaccctggaagagaaggactacccgggc
>EMBOSS_003
cgcgccttcgccgccggtggcctgcactggggggttctgaccgagggcaggatcggccgc
aggggcccggtgctgatcgtcgcccaccacctgaccctgctg
>EMBOSS_004
ctgcagaaggacttaatgcacaccctgttcaagcggggtaaacccgagctgggcatcctg
ttcggccagcgcgtgccggccttgtcgaccggctacggcctg
>EMBOSS_005
ttcctctcctacctgcgctacctgaacgtgccagaagagtccagcggcgaacgcagcgcc
ggcaccgacctgcgctcccccttcctgcggctgtgaggtgag
>EMBOSS_006
gccgacgcgtgcgaccataccgaccgcctggacatccgcagcaccatgttccccctgcgc
gagctcatccgcgcggaggcgatcatctacgacgagggcgtc
>EMBOSS_007
ccgcacctgcgcctgctgaccgtgaacgccattccggccaattggatcacctcgtgcctg
ctggtgggcatcaagggcgggaccgaggccggcttcctggtc
>EMBOSS_008
ggcggcctggcgcctcgctatcgtgccaactgcatcttcgcgctgctgcggcggccgctg
gacctgccggatgcggaggtcgccgagagtgacccggttggg
>EMBOSS_009
aagggcccgctgctctcagggaacgtcacgcgcgcgtacgtcggcgcggaagccgccgcg
gttgtggccctgtcgctgctgcgggactatgccgtagagacg
>EMBOSS_010
gtcgacggtaaggccgtggcgacctcgttccaggccctggaacttgagggctccacctcg
ggaaaagagctgatgatccgttacgtaagcggccgccgtcag
>EMBOSS_011
cggcgcgcggcactcccggtctcgttcgccccgcggaactggcacctgtggacgatccgc
caagtcgagaagtaaggccacgccctcacgggccgcaagatc
>EMBOSS_012
tatcaggcccagctcgagcaacaccatccgtgcagctgactcggccgtaattggcagcat
ctttcgatcttggccccgaagggtaagcgcttgctggcggtg
>EMBOSS_013
ctgatctacacccatgcccagaccctagtgggcccgcacaaggcgcaccaacgttgaact
ggctgagaccagtgggaaccgaaacgctacgggggcctcctg
>EMBOSS_014
gccatggccaccaacgaagatggctgcgccatccgcagcctccagcaggacgcgggcgag
acggaccaaccgctgcacggcgacgtgatgaacattttcgtc
>EMBOSS_015
cgccagagctcgcgcggcgaggcgacccagggcgcgctgcagtggggacaggtcaacgcg
ccgctggacttcgcgagcaacctgcagatgctcattgagctg
>EMBOSS_016
ctgggcgcgtcgctggagggcgaccacggcgtggcgcagaaagctaatgccagtgatggt
gtcgatacccgactgcctgcgatgtgggccgacaagccgatg
>EMBOSS_017
ctcggcttcagccccacccctgcgagcctggacgtgggcgctaagttcggcctctcgggc


  [Part of this file has been deleted for brevity]

>EMBOSS_084
ctgcgccacctgcgcggggaaaacggcatcgccacgatgtcggagatcggtgagtacgcg
agcaagcggggcatggaagccgaggccttcctgagcacactg
>EMBOSS_085
cactactacatccgcctgctgctgcaggccaccatcttcctggtcagccgcacgcgcacc
ggcgtattgattatctgtcgctttgagccggtgtttaagacc
>EMBOSS_086
actgccgagatcaagcagtacggtgcgccgccggcaccgggtgacgccctcggcgaccgc
gactgccgcggcgccgtgggtctgctgagccgccaatccgtc
>EMBOSS_087
cggaggaacaccagcgacatctatgaatggttcctgcagctggccaccgtgtcgctgatc
gccgaggagctcatcaacttccgtaccggccagaatgcccgc
>EMBOSS_088
gggatcctggacgaagcggccgccttctcgaaggagaacagaagctactatccggacggc
ctgtacacccacgtgtacaagcgcaacgagcaatggcggaac
>EMBOSS_089
gcgctgctgcgcgcccgctcgaaatgggatcgctacgagaacatcgccaagtacctgatg
aaggaggaggcagacgccgaccaggaacaggtcaccctcctg
>EMBOSS_090
ccgatcgacggctacggtaccaacctgtacgccccgatgccgcatctgggcaggagcgac
cccccgcgcgccctcgggcccccaattcaacagatcgctcgc
>EMBOSS_091
gcgaaccactcgaacgttctggtgatggcgcataccaattacaaccgcgacgccggccgt
atcccctaccaaccgagtcgacacaccggcgaggccggcgat
>EMBOSS_092
tccatcgagaaggccatcccgccggtccgtatcaaggggctggccggccgcccgtgcctc
ctaggccgggcgagcctagcgaccatcgcctatgacgccagc
>EMBOSS_093
attctgcccgacgaagacctctacgagatccgcggcttcatgcacaaggccgggcatgcg
gacccgggcgacgaacatatcaccgtgccgctcaggcaccgg
>EMBOSS_094
cgcgtctacccgcgtcaggacgcgctgaccgccgtcctggtgaaccgccttgacaatttc
ctgaccctgggcaaccagatgctggagctcaacgtccaattc
>EMBOSS_095
gacctgatggagcatttcagctcgtacctgtccctggccggcggcctcttaggcataaag
cgcaccgccccgctatcccgtatcgggacggccctggatagc
>EMBOSS_096
tgactggtcagctacggccgcttcctgctcatcgccccgctgggtctgcggacggagttc
gaacagctgtccctgggcggcgagccgggcccggccgaccgc
>EMBOSS_097
gcccatcggggtcgctgcgtgaatccgtgcgttggagcgcggcgcgcctgcgaaaacctg
ccgctgtcgccggcggtgctgctggaggtggtccgcagcgaa
>EMBOSS_098
cgcgcccctatggaacgcctgttcgcggcgttcgcgatcgccatcctggggatcatggtg
ttcgccatgctggacatcagcatcgaagagcgtttcccgctg
>EMBOSS_099
gcgaagtgccgcaccttcgtgggcagctacacgattcagagtttggacacccgggagacg
aagcagaccgtcatcgatgaggagaccaagaccaaattgacc
>EMBOSS_100
ctcggccggcaactgcggcgcgaaccgatgccgccctacgcggccctgcgttagatggac
ctcgcccccgcccgcgaccgagtcgcgctcgacacggtcgcg

Data files

**************** EDIT HERE ****************

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

See also

Program nameDescription
biosed Replace or delete sequence sections
codcopy Reads and writes a codon usage table
cutseq Removes a specified section from a sequence
degapseq Removes gap characters from sequences
descseq Alter the name or description of a sequence
entret Reads and writes (returns) flatfile entries
extractfeat Extract features from a sequence
extractseq Extract regions from a sequence
listor Write a list file of the logical OR of two sets of sequences
makeprotseq Creates random protein sequences
maskfeat Mask off features of a sequence
maskseq Mask off regions of a sequence
newseq Type in a short new sequence
noreturn Removes carriage return from ASCII files
notseq Exclude a set of sequences and write out the remaining ones
nthseq Writes one sequence from a multiple set of sequences
pasteseq Insert one sequence into another
revseq Reverse and complement a sequence
seqret Reads and writes (returns) sequences
seqretsplit Reads and writes (returns) sequences in individual files
skipseq Reads and writes (returns) sequences, skipping first few
splitter Split a sequence into (overlapping) smaller sequences
trimest Trim poly-A tails off EST sequences
trimseq Trim ambiguous bits off the ends of sequences
union Reads sequence fragments and builds one sequence
vectorstrip Strips out DNA between a pair of vector sequences
yank Reads a sequence range, appends the full USA to a list file

Author(s)

**************** EDIT HERE ****************

History

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments

None