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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) | |
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 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 |
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 |
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 |