cusp 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 a codon usage table from nucleotide sequence(s) Description cusp calculates a codon usage table for one or more nucleotide coding sequences and writes the table to file. The codon usage table gives for each codon: i. Sequence of the codon. ii. The encoded amino acid. iii. The proportion of usage of the codon among its redundant set, i.e. the set of codons which code for this codon's amino acid. iv. The expected number of codons, given the input sequence(s), per 1000 bases. v. The observed number of codons in the input sequences. Usage Here is a sample session with cusp 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 from nucleotide sequence(s) Input nucleotide sequence(s): tembl:x13776 Output file [x13776.cusp]: Go to the input files for this example Go to the output files for this example Command line arguments Create a codon usage table from nucleotide sequence(s) Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-sequence] seqall Nucleotide sequence(s) filename and optional format, or reference (input USA) [-outfile] outfile [*.cusp] Output file name Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-sequence" associated qualifiers -sbegin1 integer Start of each sequence to be used -send1 integer End of each sequence to be used -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 -sdbname1 string Database name -sid1 string Entryname -ufo1 string UFO features -fformat1 string Features format -fopenfile1 string Features file name "-outfile" associated qualifiers -odirectory2 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 Input file format Input files for usage example 'tembl:x13776' is a sequence entry in the example nucleic acid database 'tembl' Database entry: tembl:x13776 ID X13776; SV 1; linear; genomic DNA; STD; PRO; 2167 BP. XX AC X13776; M43175; XX DT 19-APR-1989 (Rel. 19, Created) DT 14-NOV-2006 (Rel. 89, Last updated, Version 24) 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; Gammaproteobacteria; Pseudomonadales; OC 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 DOI; 10.1016/0014-5793(89)80249-2. RX PUBMED; 2495988. RA Lowe N., Rice P.M., Drew R.E.; RT "Nucleotide sequence of the aliphatic amidase regulator gene (amiR) of RT Pseudomonas aeruginosa"; RL FEBS Lett. 246(1-2):39-43(1989). XX RN [3] RP 1-1292 RX PUBMED; 1907262. RA Wilson S., Drew R.; RT "Cloning and DNA sequence 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(16):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 GOA; Q51417. DR InterPro; IPR003211; AmiSUreI_transpt. DR UniProtKB/Swiss-Prot; Q51417; AMIS_PSEAE. [Part of this file has been deleted for brevity] FT /replace="" FT /note="ClaI fragment deleted in pSW36, constitutive FT phenotype" 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 // Output file format Output files for usage example File: x13776.cusp #CdsCount: 1 #Coding GC 67.79% #1st letter GC 67.88% #2nd letter GC 46.89% #3rd letter GC 88.60% #Codon AA Fraction Frequency 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 shown reads a single CDS from Pseudomonas aeruginosa which has a very high GC content and a strong coding bias, as shown by the codons for Alanine where those ending with G or C are used almost exclusively. The columns are as follows: i. "Codon" (sequence of the codon). ii. "AA" (the encoded amino acid). iii. "Fraction" (the proportion of usage of the codon among its redundant set, i.e. the set of codons which code for this codon's amino acid). iv. "Frequency" (the expected number of codons, given the input sequence(s), per 1000 bases). This will be an extrapolation if the sequence is shorter than 1000 bases. v. "Number" (the observed number of codons in the input sequences). If multiple sequences are input then the statistics are given for all of the sequences together, not individually. Data files cusp reads a codon usage file as a template for it's output file. The data in this table is ignored entirely. This functionality is hard-coded and invisible to the user. EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by the EMBOSS environment variable EMBOSS_DATA. To see the available EMBOSS data files, run: % embossdata -showall To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run: % embossdata -fetch -file Exxx.dat Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata". The directories are searched in the following order: * . (your current directory) * .embossdata (under your current directory) * ~/ (your home directory) * ~/.embossdata Notes None. References None. Warnings None. Diagnostic Error Messages None. Exit status Always exits with status 0. Known bugs None. See also Program name Description cai Calculate codon adaptation index chips Calculates Nc codon usage statistic codcmp Codon usage table comparison codcopy Copy and reformat a codon usage table syco Draw synonymous codon usage statistic plot for a nucleotide sequence Author(s) Alan Bleasby European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Please report all bugs to the EMBOSS bug team (emboss-bug (c) 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