                                 makenucseq



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   http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

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Function

   Create random nucleotide sequences

Description

   makenucseq writes an output file with a set of random nucleotide
   sequences. The sequence composition is defined from reading a codon
   usage file: the sequences are created with triplet frequencies matching
   those given in the file, with the end trimmed to be in the correct
   reading frame. The number of sequences to create and length of each
   sequence is specified. Optionally, a user-defined string may be
   inserted into each output sequence at a specified position

Algorithm

Usage

   Here is a sample session with makenucseq


% makenucseq
Create 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
Create 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

Create random nucleotide sequences
Version: EMBOSS:6.6.0.0

   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)
*  -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 first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to 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 and exit. 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
   -version            boolean    Report version number and exit


Input file format

   makenucseq reads an optional codon usage file.

   The input is a standard EMBOSS codon usage query.

   Data can also be read from codon usage output in any supported format
   written by an EMBOSS or third party application.

   The input format can be specified by using the command-line qualifier
   -format xxx, where 'xxx' is replaced by the name of the required
   format. The available format names are: emboss, cut, gcg, cutg, cutgaa,
   spsum, cherry, transterm, codehop, staden and numstaden.

Output file format

   makenucseq writes a sequence file with the number of sequences
   requested.

  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
gcgcggcagggcttcatctgactgctgttcggcgtgcgcg
>EMBOSS_002
gacgccggcgcgaccgagcggcaccgcttcgtccgaggaggcggcggcttcaccctcgtg
gccttcgacgacagcaccctggaagagaaggactacccgg
>EMBOSS_003
cgcgccttcgccgccggtggcctgcactggggggttctgaccgagggcaggatcggccgc
aggggcccggtgctgatcgtcgcccaccacctgaccctgc
>EMBOSS_004
ctgcagaaggacttaatgcacaccctgttcaagcggggtaaacccgagctgggcatcctg
ttcggccagcgcgtgccggccttgtcgaccggctacggcc
>EMBOSS_005
ttcctctcctacctgcgctacctgaacgtgccagaagagtccagcggcgaacgcagcgcc
ggcaccgacctgcgctcccccttcctgcggctgtgaggtg
>EMBOSS_006
gccgacgcgtgcgaccataccgaccgcctggacatccgcagcaccatgttccccctgcgc
gagctcatccgcgcggaggcgatcatctacgacgagggcg
>EMBOSS_007
ccgcacctgcgcctgctgaccgtgaacgccattccggccaattggatcacctcgtgcctg
ctggtgggcatcaagggcgggaccgaggccggcttcctgg
>EMBOSS_008
ggcggcctggcgcctcgctatcgtgccaactgcatcttcgcgctgctgcggcggccgctg
gacctgccggatgcggaggtcgccgagagtgacccggttg
>EMBOSS_009
aagggcccgctgctctcagggaacgtcacgcgcgcgtacgtcggcgcggaagccgccgcg
gttgtggccctgtcgctgctgcgggactatgccgtagaga
>EMBOSS_010
gtcgacggtaaggccgtggcgacctcgttccaggccctggaacttgagggctccacctcg
ggaaaagagctgatgatccgttacgtaagcggccgccgtc
>EMBOSS_011
cggcgcgcggcactcccggtctcgttcgccccgcggaactggcacctgtggacgatccgc
caagtcgagaagtaaggccacgccctcacgggccgcaaga
>EMBOSS_012
tatcaggcccagctcgagcaacaccatccgtgcagctgactcggccgtaattggcagcat
ctttcgatcttggccccgaagggtaagcgcttgctggcgg
>EMBOSS_013
ctgatctacacccatgcccagaccctagtgggcccgcacaaggcgcaccaacgttgaact
ggctgagaccagtgggaaccgaaacgctacgggggcctcc
>EMBOSS_014
gccatggccaccaacgaagatggctgcgccatccgcagcctccagcaggacgcgggcgag
acggaccaaccgctgcacggcgacgtgatgaacattttcg
>EMBOSS_015
cgccagagctcgcgcggcgaggcgacccagggcgcgctgcagtggggacaggtcaacgcg
ccgctggacttcgcgagcaacctgcagatgctcattgagc
>EMBOSS_016
ctgggcgcgtcgctggagggcgaccacggcgtggcgcagaaagctaatgccagtgatggt
gtcgatacccgactgcctgcgatgtgggccgacaagccga
>EMBOSS_017
ctcggcttcagccccacccctgcgagcctggacgtgggcgctaagttcggcctctcgggc


  [Part of this file has been deleted for brevity]

>EMBOSS_084
ctgcgccacctgcgcggggaaaacggcatcgccacgatgtcggagatcggtgagtacgcg
agcaagcggggcatggaagccgaggccttcctgagcacac
>EMBOSS_085
cactactacatccgcctgctgctgcaggccaccatcttcctggtcagccgcacgcgcacc
ggcgtattgattatctgtcgctttgagccggtgtttaaga
>EMBOSS_086
actgccgagatcaagcagtacggtgcgccgccggcaccgggtgacgccctcggcgaccgc
gactgccgcggcgccgtgggtctgctgagccgccaatccg
>EMBOSS_087
cggaggaacaccagcgacatctatgaatggttcctgcagctggccaccgtgtcgctgatc
gccgaggagctcatcaacttccgtaccggccagaatgccc
>EMBOSS_088
gggatcctggacgaagcggccgccttctcgaaggagaacagaagctactatccggacggc
ctgtacacccacgtgtacaagcgcaacgagcaatggcgga
>EMBOSS_089
gcgctgctgcgcgcccgctcgaaatgggatcgctacgagaacatcgccaagtacctgatg
aaggaggaggcagacgccgaccaggaacaggtcaccctcc
>EMBOSS_090
ccgatcgacggctacggtaccaacctgtacgccccgatgccgcatctgggcaggagcgac
cccccgcgcgccctcgggcccccaattcaacagatcgctc
>EMBOSS_091
gcgaaccactcgaacgttctggtgatggcgcataccaattacaaccgcgacgccggccgt
atcccctaccaaccgagtcgacacaccggcgaggccggcg
>EMBOSS_092
tccatcgagaaggccatcccgccggtccgtatcaaggggctggccggccgcccgtgcctc
ctaggccgggcgagcctagcgaccatcgcctatgacgcca
>EMBOSS_093
attctgcccgacgaagacctctacgagatccgcggcttcatgcacaaggccgggcatgcg
gacccgggcgacgaacatatcaccgtgccgctcaggcacc
>EMBOSS_094
cgcgtctacccgcgtcaggacgcgctgaccgccgtcctggtgaaccgccttgacaatttc
ctgaccctgggcaaccagatgctggagctcaacgtccaat
>EMBOSS_095
gacctgatggagcatttcagctcgtacctgtccctggccggcggcctcttaggcataaag
cgcaccgccccgctatcccgtatcgggacggccctggata
>EMBOSS_096
tgactggtcagctacggccgcttcctgctcatcgccccgctgggtctgcggacggagttc
gaacagctgtccctgggcggcgagccgggcccggccgacc
>EMBOSS_097
gcccatcggggtcgctgcgtgaatccgtgcgttggagcgcggcgcgcctgcgaaaacctg
ccgctgtcgccggcggtgctgctggaggtggtccgcagcg
>EMBOSS_098
cgcgcccctatggaacgcctgttcgcggcgttcgcgatcgccatcctggggatcatggtg
ttcgccatgctggacatcagcatcgaagagcgtttcccgc
>EMBOSS_099
gcgaagtgccgcaccttcgtgggcagctacacgattcagagtttggacacccgggagacg
aagcagaccgtcatcgatgaggagaccaagaccaaattga
>EMBOSS_100
ctcggccggcaactgcggcgcgaaccgatgccgccctacgcggccctgcgttagatggac
ctcgcccccgcccgcgaccgagtcgcgctcgacacggtcg

Data files

   None.

Notes

   None.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

   Program name     Description
   aligncopy        Read and write alignments
   aligncopypair    Read and write pairs from alignments
   biosed           Replace or delete sequence sections
   codcopy          Copy and reformat a codon usage table
   cutseq           Remove a section from a sequence
   degapseq         Remove non-alphabetic (e.g. gap) characters from sequences
   descseq          Alter the name or description of a sequence
   entret           Retrieve sequence entries from flatfile databases and files
   extractalign     Extract regions from a sequence alignment
   extractfeat      Extract features from sequence(s)
   extractseq       Extract regions from a sequence
   featcopy         Read and write a feature table
   featmerge        Merge two overlapping feature tables
   featreport       Read and write a feature table
   feattext         Return a feature table original text
   listor           Write a list file of the logical OR of two sets of sequences
   makeprotseq      Create random protein sequences
   maskambignuc     Mask all ambiguity characters in nucleotide sequences with
                    N
   maskambigprot    Mask all ambiguity characters in protein sequences with X
   maskfeat         Write a sequence with masked features
   maskseq          Write a sequence with masked regions
   newseq           Create a sequence file from a typed-in sequence
   nohtml           Remove mark-up (e.g. HTML tags) from an ASCII text file
   noreturn         Remove carriage return from ASCII files
   nospace          Remove whitespace from an ASCII text file
   notab            Replace tabs with spaces in an ASCII text file
   notseq           Write to file a subset of an input stream of sequences
   nthseq           Write to file a single sequence from an input stream of
                    sequences
   nthseqset        Read and write (return) one set of sequences from many
   pasteseq         Insert one sequence into another
   revseq           Reverse and complement a nucleotide sequence
   seqcount         Read and count sequences
   seqret           Read and write (return) sequences
   seqretsetall     Read and write (return) many sets of sequences
   seqretsplit      Read sequences and write them to individual files
   sizeseq          Sort sequences by size
   skipredundant    Remove redundant sequences from an input set
   skipseq          Read and write (return) sequences, skipping first few
   splitsource      Split sequence(s) into original source sequences
   splitter         Split sequence(s) into smaller sequences
   trimest          Remove poly-A tails from nucleotide sequences
   trimseq          Remove unwanted characters from start and end of sequence(s)
   trimspace        Remove extra whitespace from an ASCII text file
   union            Concatenate multiple sequences into a single sequence
   vectorstrip      Remove vectors from the ends of nucleotide sequence(s)
   yank             Add a sequence reference (a full USA) to a list file

Author(s)

   This application was contributed by Henrikki Almusa, Medicel, Helsinki,
   Finland

   Please report all bugs to the EMBOSS bug team
   (emboss-bug (c) emboss.open-bio.org) not to the original author.

History

Target users

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

Comments

   None
