|   | 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
| 
   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  [ | 
| 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) | |||
| >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 | 
| >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 | 
| 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 |