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cusp |
The output file can be used as a codon usage table in other applications.
This example uses only one input sequence. The normal use would be to use a set of coding sequences as the input.
% cusp -sbeg 135 -send 1292 Create a codon usage table Input sequence(s): tembl:paamir Output file [paamir.cusp]: |
Go to the input files for this example
Go to the output files for this example
Mandatory qualifiers:
[-sequence] seqall Sequence database USA
[-outfile] outfile Output file name
Optional qualifiers: (none)
Advanced qualifiers:
-cfile codon Codon usage table name
Associated qualifiers:
"-sequence" related qualifiers
-sbegin1 integer First base used
-send1 integer Last base used, def=seq length
-sreverse1 boolean Reverse (if DNA)
-sask1 boolean Ask for begin/end/reverse
-snucleotide1 boolean Sequence is nucleotide
-sprotein1 boolean Sequence is protein
-slower1 boolean Make lower case
-supper1 boolean Make upper case
-sformat1 string Input sequence format
-sopenfile1 string Input filename
-sdbname1 string Database name
-sid1 string Entryname
-ufo1 string UFO features
-fformat1 string Features format
-fopenfile1 string Features file name
"-outfile" related qualifiers
-odirectory2 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 required and optional values
-debug boolean Write debug output to program.dbg
-acdlog boolean Write ACD processing log to program.acdlog
-acdpretty boolean Rewrite ACD file as program.acdpretty
-acdtable boolean Write HTML table of options
-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 deaths
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| Mandatory qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-sequence] (Parameter 1) |
Sequence database USA | Readable sequence(s) | Required |
| [-outfile] (Parameter 2) |
Output file name | Output file | <sequence>.cusp |
| Optional qualifiers | Allowed values | Default | |
| (none) | |||
| Advanced qualifiers | Allowed values | Default | |
| -cfile | Codon usage table name | Codon usage file in EMBOSS data path | Ehum.cut |
ID PAAMIR standard; DNA; PRO; 2167 BP.
XX
AC X13776; M43175;
XX
SV X13776.1
XX
DT 19-APR-1989 (Rel. 19, Created)
DT 17-FEB-1997 (Rel. 50, Last updated, Version 22)
XX
DE Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation
XX
KW aliphatic amidase regulator; amiC gene; amiR gene.
XX
OS Pseudomonas aeruginosa
OC Bacteria; Proteobacteria; gamma subdivision; Pseudomonadaceae; Pseudomonas.
XX
RN [1]
RP 1167-2167
RA Rice P.M.;
RT ;
RL Submitted (16-DEC-1988) to the EMBL/GenBank/DDBJ databases.
RL Rice P.M., EMBL, Postfach 10-2209, Meyerhofstrasse 1, 6900 Heidelberg, FRG.
XX
RN [2]
RP 1167-2167
RX MEDLINE; 89211409.
RA Lowe N., Rice P.M., Drew R.E.;
RT "Nucleotide sequence of the aliphatic amidase regulator gene of Pseudomonas
RT aeruginosa";
RL FEBS Lett. 246:39-43(1989).
XX
RN [3]
RP 1-1292
RX MEDLINE; 91317707.
RA Wilson S., Drew R.;
RT "Cloning and DNA seqence of amiC, a new gene regulating expression of the
RT Pseudomonas aeruginosa aliphatic amidase, and purification of the amiC
RT product.";
RL J. Bacteriol. 173:4914-4921(1991).
XX
RN [4]
RP 1-2167
RA Rice P.M.;
RT ;
RL Submitted (04-SEP-1991) to the EMBL/GenBank/DDBJ databases.
RL Rice P.M., EMBL, Postfach 10-2209, Meyerhofstrasse 1, 6900 Heidelberg, FRG.
XX
DR SWISS-PROT; P10932; AMIR_PSEAE.
DR SWISS-PROT; P27017; AMIC_PSEAE.
DR SWISS-PROT; Q51417; AMIS_PSEAE.
[Part of this file has been deleted for brevity]
FT phenotype"
FT /replace=""
FT /gene="amiC"
FT misc_feature 1
FT /note="last base of an XhoI site"
FT misc_feature 648..653
FT /note="end of 658bp XhoI fragment, deletion in pSW3 causes
FT constitutive expression of amiE"
FT conflict 1281
FT /replace="g"
FT /citation=[3]
XX
SQ Sequence 2167 BP; 363 A; 712 C; 730 G; 362 T; 0 other;
ggtaccgctg gccgagcatc tgctcgatca ccaccagccg ggcgacggga actgcacgat 60
ctacctggcg agcctggagc acgagcgggt tcgcttcgta cggcgctgag cgacagtcac 120
aggagaggaa acggatggga tcgcaccagg agcggccgct gatcggcctg ctgttctccg 180
aaaccggcgt caccgccgat atcgagcgct cgcacgcgta tggcgcattg ctcgcggtcg 240
agcaactgaa ccgcgagggc ggcgtcggcg gtcgcccgat cgaaacgctg tcccaggacc 300
ccggcggcga cccggaccgc tatcggctgt gcgccgagga cttcattcgc aaccgggggg 360
tacggttcct cgtgggctgc tacatgtcgc acacgcgcaa ggcggtgatg ccggtggtcg 420
agcgcgccga cgcgctgctc tgctacccga ccccctacga gggcttcgag tattcgccga 480
acatcgtcta cggcggtccg gcgccgaacc agaacagtgc gccgctggcg gcgtacctga 540
ttcgccacta cggcgagcgg gtggtgttca tcggctcgga ctacatctat ccgcgggaaa 600
gcaaccatgt gatgcgccac ctgtatcgcc agcacggcgg cacggtgctc gaggaaatct 660
acattccgct gtatccctcc gacgacgact tgcagcgcgc cgtcgagcgc atctaccagg 720
cgcgcgccga cgtggtcttc tccaccgtgg tgggcaccgg caccgccgag ctgtatcgcg 780
ccatcgcccg tcgctacggc gacggcaggc ggccgccgat cgccagcctg accaccagcg 840
aggcggaggt ggcgaagatg gagagtgacg tggcagaggg gcaggtggtg gtcgcgcctt 900
acttctccag catcgatacg cccgccagcc gggccttcgt ccaggcctgc catggtttct 960
tcccggagaa cgcgaccatc accgcctggg ccgaggcggc ctactggcag accttgttgc 1020
tcggccgcgc cgcgcaggcc gcaggcaact ggcgggtgga agacgtgcag cggcacctgt 1080
acgacatcga catcgacgcg ccacaggggc cggtccgggt ggagcgccag aacaaccaca 1140
gccgcctgtc ttcgcgcatc gcggaaatcg atgcgcgcgg cgtgttccag gtccgctggc 1200
agtcgcccga accgattcgc cccgaccctt atgtcgtcgt gcataacctc gacgactggt 1260
ccgccagcat gggcggggga ccgctcccat gagcgccaac tcgctgctcg gcagcctgcg 1320
cgagttgcag gtgctggtcc tcaacccgcc gggggaggtc agcgacgccc tggtcttgca 1380
gctgatccgc atcggttgtt cggtgcgcca gtgctggccg ccgccggaag ccttcgacgt 1440
gccggtggac gtggtcttca ccagcatttt ccagaatggc caccacgacg agatcgctgc 1500
gctgctcgcc gccgggactc cgcgcactac cctggtggcg ctggtggagt acgaaagccc 1560
cgcggtgctc tcgcagatca tcgagctgga gtgccacggc gtgatcaccc agccgctcga 1620
tgcccaccgg gtgctgcctg tgctggtatc ggcgcggcgc atcagcgagg aaatggcgaa 1680
gctgaagcag aagaccgagc agctccagga ccgcatcgcc ggccaggccc ggatcaacca 1740
ggccaaggtg ttgctgatgc agcgccatgg ctgggacgag cgcgaggcgc accagcacct 1800
gtcgcgggaa gcgatgaagc ggcgcgagcc gatcctgaag atcgctcagg agttgctggg 1860
aaacgagccg tccgcctgag cgatccgggc cgaccagaac aataacaaga ggggtatcgt 1920
catcatgctg ggactggttc tgctgtacgt tggcgcggtg ctgtttctca atgccgtctg 1980
gttgctgggc aagatcagcg gtcgggaggt ggcggtgatc aacttcctgg tcggcgtgct 2040
gagcgcctgc gtcgcgttct acctgatctt ttccgcagca gccgggcagg gctcgctgaa 2100
ggccggagcg ctgaccctgc tattcgcttt tacctatctg tgggtggccg ccaaccagtt 2160
cctcgag 2167
//
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# CUSP codon usage file # Codon Amino acid Fract /1000 Number GCA A 0.077 7.772 3 GCC A 0.462 46.632 18 GCG A 0.462 46.632 18 GCT A 0.000 0.000 0 TGC C 1.000 10.363 4 TGT C 0.000 0.000 0 GAC D 0.864 49.223 19 GAT D 0.136 7.772 3 GAA E 0.269 18.135 7 GAG E 0.731 49.223 19 TTC F 1.000 28.497 11 TTT F 0.000 0.000 0 GGA G 0.062 5.181 2 GGC G 0.719 59.585 23 GGG G 0.125 10.363 4 GGT G 0.094 7.772 3 CAC H 0.727 20.725 8 CAT H 0.273 7.772 3 ATA I 0.000 0.000 0 ATC I 0.800 41.451 16 ATT I 0.200 10.363 4 AAA K 0.000 0.000 0 AAG K 1.000 5.181 2 CTA L 0.000 0.000 0 CTC L 0.269 18.135 7 CTG L 0.577 38.860 15 CTT L 0.000 0.000 0 TTA L 0.000 0.000 0 TTG L 0.154 10.363 4 ATG M 1.000 15.544 6 AAC N 1.000 28.497 11 AAT N 0.000 0.000 0 CCA P 0.074 5.181 2 CCC P 0.222 15.544 6 CCG P 0.630 44.041 17 CCT P 0.074 5.181 2 CAA Q 0.062 2.591 1 CAG Q 0.938 38.860 15 AGA R 0.000 0.000 0 AGG R 0.029 2.591 1 CGA R 0.000 0.000 0 CGC R 0.629 56.995 22 CGG R 0.314 28.497 11 CGT R 0.029 2.591 1 AGC S 0.304 18.135 7 AGT S 0.087 5.181 2 TCA S 0.000 0.000 0 TCC S 0.261 15.544 6 TCG S 0.304 18.135 7 TCT S 0.043 2.591 1 ACA T 0.000 0.000 0 ACC T 0.733 28.497 11 ACG T 0.267 10.363 4 ACT T 0.000 0.000 0 GTA V 0.030 2.591 1 GTC V 0.394 33.679 13 GTG V 0.576 49.223 19 GTT V 0.000 0.000 0 TGG W 1.000 12.953 5 TAC Y 0.619 33.679 13 TAT Y 0.381 20.725 8 TAA * 0.000 0.000 0 TAG * 0.000 0.000 0 TGA * 1.000 2.591 1 |
The example usage read in a single CDS from Pseudomonas aeruginosa which has a very high GC content ands a strong coding bias, as shown by the codons for Alanine where those ending with G or C are used almost exclusively.
The 'Fract' column gives the faction of all amino acids coded for by this codon triplet.
The /1000 column represents the number of codons, given the input sequence(s), there are per 1000 bases. This will be an extrapolation if the sequence is shorter than 1000 bases.
If multiple sequences are input then the statistics are given for all of the sequences together, not individually.
| Program name | Description |
|---|---|
| cai | CAI codon adaptation index |
| chips | Codon usage statistics |
| codcmp | Codon usage table comparison |
| syco | Synonymous codon usage Gribskov statistic plot |