Coding Sequence Analysis Tools
CLARK LAB at the University of Notre Dame

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Gene Sequence   ||   Codon Usage   ||   Random Reverse Translation

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Gene Sequence:

(1) Must follow FASTA formatting.
(2) Each sequence must contain 3n base pairs, where n is a non-negative integer.
(3) Can submit multiple sequences as one job.
(4) Cannot exceed 25000 characters in length. If you would like to submit a larger job, please contact us.

Example:

>b0587 ferric enterobactin (enterochelin) transport (fepE) {Escherichia coli K12-MG1655} ATGTCATCACTGAATATTAAACAGGGAAGTGACGCTCATTTTCCCGATTATCCTCTGGCG TCGCCCAGTAATAATGAAATTGATTTACTTAATCTAATCTCAGTTTTATGGCGGGCCAAA AAAACGGTCATGGCGGTCGTTTTTGCGTTTGCCTGCGCAGGCTTGCTGATCTCTTTCATC CTGCCGCAAAAATGGACCAGCGCGGCGGTTGTCACGCCTCCAGAACCTGTTCAGTGGCAA GAGTTGGAGAAATCATTCACTAAGCTTCGTGTGCTGGATCTGGATATCAAAATTGATCGT ACAGAAGCATTTAACCTGTTTATCAAGAAGTTTCAGTCGGTTAGCTTGCTGGAAGAGTAC CTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGAT TTGCATCGCGCAATTGTCGCATTGAGCGAAAAAATGAAAGCGGTTGATGACAATGCCAGT AAGAAAAAAGATGAACCGTCACTGTATACCTCCTGGACGCTAAGTTTTACCGCGCCAACC AGTGAAGAGGCGCAGACCGTTTTGAGCGGGTATATCGATTATATCTCTACGTTGGTGGTG AAAGAGTCGCTAGAAAACGTCCGTAATAAACTGGAGATCAAAACCCAGTTTGAAAAAGAA AAACTGGCTCAGGATCGCATTAAAACGAAAAATCAACTTGATGCAAACATTCAGCGCCTC AATTATTCACTCGACATTGCCAACGCGGCAGGAATTAAAAAGCCCGTTTACAGTAATGGT CAGGCCGTTAAAGATGACCCCGATTTTTCTATTTCTCTCGGTGCAGACGGTATTGAACGC AAACTGGAAATAGAAAAAGCGGTCACTGACGTTGCGGAACTGAACGGTGAATTACGTAAT CGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAATTTTACGCCG TTTAAATATCAGTTAAGCCCGTCATTGCCAGTGAAAAAAGACGGTCCGGGTAAGGCGATT ATTGTGATCCTTTCCGCGTTGATCGGCGGGATGGTGGCTTGTGGTGGCGTGCTGTTGCGC TATGCGATGGCATCCAGAAAACAGGATGCCATGATGGCAGACCACTTAGTTTAA >b0588 ATP-binding component of ferric enterobactin transport (fepC) {Escherichia coli K12-MG1655} ATGACCGAATCAGTAGCCCGTTTGCGCGGCGAACAGTTAACCCTGGGATATGGCAAATAT ACCGTTGCGGAAAATCTGACTGTAGAAATACCTGATGGTCACTTCACGGCAATTATCGGG CCAAATGGCTGCGGTAAATCCACGTTACTGCGTACCTTAAGCCGCCTGATGACGCCTGCT CATGGGCATGTCTGGCTGGATGGCGAGCACATTCAACATTACGCCAGTAAAGAGGTTGCA CGCCGGATTGGTCTGTTGGCGCAAAATGCTACCACGCCGGGCGATATCACCGTGCAGGAG CTGGTGGCGCGTGGACGTTATCCGCATCAACCGCTGTTTACCCGCTGGCGCAAAGAGGAT GAAGAAGCGGTAACGAAAGCAATGCAGGCCACGGGAATAACTCATCTGGCAGATCAAAGC GTGGATACCCTTTCTGGCGGACAACGCCAGCGAGCGTGGATCGCGATGGTGCTGGCCCAG GAAACGGCAATTATGCTGCTCGACGAACCCACGACCTGGCTGGATATCAGTCATCAGATT GATTTGCTGGAGTTGTTAAGCGAACTGAACCGCGAAAAAGGCTATACCCTGGCGGCGGTG CTGCACGATCTTAATCAGGCCTGTCGTTACGCCAGCCATTTGATTGCATTGCGGGAAGGG AAAATTGTTGCTCAGGGAGCGCCGAAGGAGATTGTCACTGCTGAACTGATTGAGCGCATT TATGGTCTGCGCTGCATGATCATTGACGATCCAGTTGCCGGAACGCCGCTTGTGGTGCCG CTCGGACGAACGGCACCTTCAACCGCAAATAGTTAA

Click here for a sample results page based on the above example sequence and ecoli codon usage.

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Codon Usage:

(1) All codons must be assigned a non-negative integer.
(2) Formatting must be in "Codon Usage Database" format: [triplet] [frequency per thousand codons] ([total number in ORFeome])

Example:

UUU 15.7( 26) UCU 13.9( 23) UAU 24.8( 41) UGU 9.7( 16) UUC 26.0( 43) UCC 13.3( 22) UAC 17.6( 29) UGC 12.1( 20) UUA 14.5( 24) UCA 20.6( 34) UAA 4.2( 7) UGA 0.0( 0) UUG 10.3( 17) UCG 13.9( 23) UAG 0.6( 1) UGG 14.5( 24) CUU 10.9( 18) CCU 20.0( 33) CAU 17.6( 29) CGU 19.4( 32) CUC 13.3( 22) CCC 9.1( 15) CAC 17.0( 28) CGC 3.0( 5) CUA 6.7( 11) CCA 23.0( 38) CAA 18.2( 30) CGA 6.7( 11) CUG 14.5( 24) CCG 4.2( 7) CAG 24.2( 40) CGG 10.3( 17) AUU 17.0( 28) ACU 15.7( 26) AAU 32.7( 54) AGU 9.7( 16) AUC 20.0( 33) ACC 13.3( 22) AAC 27.9( 46) AGC 18.8( 31) AUA 16.4( 27) ACA 16.4( 27) AAA 25.4( 42) AGA 16.4( 27) AUG 23.0( 38) ACG 10.3( 17) AAG 30.9( 51) AGG 17.6( 29) GUU 16.4( 27) GCU 11.5( 19) GAU 27.3( 45) GGU 18.8( 31) GUC 17.6( 29) GCC 13.9( 23) GAC 25.4( 42) GGC 10.3( 17) GUA 20.0( 33) GCA 12.1( 20) GAA 19.4( 32) GGA 14.5( 24) GUG 7.9( 13) GCG 9.7( 16) GAG 23.0( 38) GGG 10.9( 18)

OR the following format: [triplet] [number in ORFeome]

Example:

TTT 26 TCT 23 TAT 41 TGT 16 TTC 43 TCC 22 TAC 29 TGC 20 TTA 24 TCA 34 TAA 7 TGA 0 TTG 17 TCG 23 TAG 1 TGG 24 CTT 18 CCT 33 CAT 29 CGT 32 CTC 22 CCC 15 CAC 28 CGC 5 CTA 11 CCA 38 CAA 30 CGA 11 CTG 24 CCG 7 CAG 40 CGG 17 ATT 28 ACT 26 AAT 54 AGT 16 ATC 33 ACC 22 AAC 46 AGC 31 ATA 27 ACA 27 AAA 42 AGA 27 ATG 38 ACG 17 AAG 51 AGG 29 GTT 27 GCT 19 GAT 45 GGT 31 GTC 29 GCC 23 GAC 42 GGC 17 GTA 33 GCA 20 GAA 32 GGA 24 GTG 13 GCG 16 GAG 38 GGG 18

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Random Reverse Translation:

The Random Reverse Translation (RRT) option creates a control with which to compare your results. Your gene sequence is translated into an amino acid sequence. This, in turn, is converted back into nucleotides according to the selected codon usage probabilities. In all, 200 RRTs are built, processed by the Rare Codon Calculator, and then averaged. It should take approximately 15 seconds to process 1000 nucleotides.

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Please contact us with addition questions.

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Stanley D. Strycker, web designer
an SDS webPAGE