EMBOSS: makenucseq

| 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

## 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) | <*>.format
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
    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

## 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
--- | ---
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
extractalign | Extract regions from a sequence alignment
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)

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

## History

## Target users

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

## Comments

None