EMBOSS: makenucseq

| makenucseq

## Wiki

The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

Please help by correcting and extending the Wiki pages.

## 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:6.5.6.0

       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

Qualifier | Type | Description | Allowed values | Default
--- | --- | --- | --- | ---
Standard (Mandatory) qualifiers
-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. | Codon usage file in EMBOSS data path |
-amount | integer | Number of sequences created | Integer 1 or more | 100
-length | integer | Length of each sequence | Integer 1 or more | 100
-insert | string | String that is inserted into sequence | Any string |
-start | integer | Start point of inserted sequence | Integer 1 or more | 1
[-outseq] (Parameter 1) | seqoutall | Nucleotide sequence set(s) filename and optional format (output USA) | Writeable sequence(s) | <*>.format
Additional (Optional) qualifiers
-useinsert | toggle | Do you want to make an insert | Toggle value Yes/No | No
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-codonfile" associated codon qualifiers
-format | string | Data format | Any string |
"-outseq" associated seqoutall qualifiers
-osformat1 -osformat_outseq | string | Output seq format | Any string |
-osextension1 -osextension_outseq | string | File name extension | Any string |
-osname1 -osname_outseq | string | Base file name | Any string |
-osdirectory1 -osdirectory_outseq | string | Output directory | Any string |
-osdbname1 -osdbname_outseq | string | Database name to add | Any string |
-ossingle1 -ossingle_outseq | boolean | Separate file for each entry | Boolean value Yes/No | N
-oufo1 -oufo_outseq | string | UFO features | Any string |
-offormat1 -offormat_outseq | string | Features format | Any string |
-ofname1 -ofname_outseq | string | Features file name | Any string |
-ofdirectory1 -ofdirectory_outseq | string | Output directory | Any string |
General qualifiers
-auto | boolean | Turn off prompts | Boolean value Yes/No | N
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N
-warning | boolean | Report warnings | Boolean value Yes/No | Y
-error | boolean | Report errors | Boolean value Yes/No | Y
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y
-die | boolean | Report dying program messages | Boolean value Yes/No | Y
-version | boolean | Report version number and exit | Boolean value Yes/No | N

## 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 © 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