RCDI / eRCDI
Relative Codon Deoptimization Index / Expected RCDI

The RCDI server is a web-application that calculates the Relative Codon Deoptimization Index (RCDI) and an expected value of the RCDI for a set of query sequences by generating random sequences with similar G+C content and amino acid composition to the input. This expected RCDI therefore provides a direct threshold value for discerning whether the differences in the RCDI value are statistically significant and arise from the codon preferences or whether they are merely artifacts that arise from internal biases in the G+C composition and/or amino acid composition of the query sequences. Please, click here to get a quick tutorial.

HOW TO CITE: Puigbo P, Aragones L and Garcia-Vallve S. (2010) RCDI/eRCDI: a web-server to estimate codon usage deoptimization. BMC Research Notes,3:87.

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Insert your sequences in FASTA format help

>SeqA
ATGCAGAACGACGCCGGCGAATTTGTGGACTTATACGTGCCTCGGAAGTGCTCAGCCTCTAATCGCATTATAGCCGCTAAGGACCACGCTAGCATCCAGATGAATGTCGCTGAGGTAGACCGCACCACAGGGAGATTTAACGGCCAGTTTAAGACTTATGGAATATGCGGGGCCATTCGGAGAATGGGGGAGAGCGATGACAGCATCCTCAGGCTGGCGAAGGCCGACGGGATTGTTTCAAAAAACTTC
>SeqB
ATGCAGAATGACGCAGGCGAGTTTGTGGATCTATATGTGCCACGGAAGTGCTCGGCCTCCAATAGGATTATTGCCGCAAAAGACCATGCCTCTATCCAGATGAATGTTGCAGAAGTGGACCGGTCTACCGGCAGGTTTAACGGGCAGTTCAAAACGTATGGCATTTGCGGGGCTATCCGACGGATGGGTGAAAGCGATGATAGTATCCTGCGCTTAGCAAAGGCTGACGGGATTGTATCGAAGAACTTC
>SeqC
ATGCAAAACGATGCCGGCGAGTTTGTGGACCTCTATGTGCCTAGAAAATGTTCGGCTTCCAATCGTATCATTGGTGCCAAGGATCATGCCAGCATCCAGATGAACGTTGCCGAGGTTGATAAGGTGACAGGCAGGTTTAATGGCCAGTTCAAGACTTACGCGATTTGCGGCGCGATCAGACGAATGGGCGAGAGCGACGACTCAATCTTGAGGTTAGCAAAGGCCGACGGGATCGTTAGCAAAAACTTC
>SeqD
ATGGAGAATGATGCAGGGGAGAACGTCGATCTGTATGTTCCCCGCAAGTGTTCCGCCTCTAATCGTATTATTCACGCAAAAGACCACGCAAGTGTACAGCTGTCAATTGTGGATGTGGATCCCGAAACCGGAAGGCAGACTGACGGGAGTAAAACTTACGCCATTTGCGGCGAAATCCGCCGCATGGGAGAGTCTGATGACTGCATCGTCAGGTTAGCAAAAAAGGACGGAATAATCACCAAGAACTTC
>SeqE
ATGCAGAACGATGCAGGGCAGACTGTTGAGCTGTATGTACCGCGCAAGTGCAGCTCTTCAAATCGCATCATCGGGCCAAAAGACCACGCCAGCGTACAGATCGACTTTGTAGATGTCGACCCTGAAACAGGGAGGATGATCCCAGGGAAGTCCACTAGGTACGCCATCTGCGGAGCTATCCGCCGTATGGGAGAGAGCGACGACGCTATTCTACGGCTCGCCCAAAAAGATGGGTTAGTGCCACGCGATGACGTGAAGTCCAAC
>SeqF
ATGCAGAACGCCAGTGGACGAATTGTAGATTTGTACGTGCCACGTAAGTGCTCCGTCACTAATCGATTAATAAGTGCTAAGGACCACGCGTCTGTTCAGCTGAACATTGCCAAAGTCGATCCCGATACAGGGCGTATGGTGCCTGGTGAACATCTTACAGTTGCTCTTACCGGGAGCATTAGAAGGCTTGGCCTGAGCGACCAGGCTGTGTTCCGACTTGCTAAAGAAAAGGGCGCCTTGGATGATCTCCGTGGAGGAGGCGCAGTCGGTGTGGGCTCTGGTGCCAGCGGTGGTGCTGAAGAGAGAACCGAT
>SeqG
ATGGAGAATGACAAAGGGCAGCTGGTCGAGCTATATGTGCCTAGAAAATGCTCTGCTACAAATCGTATTATCAAAGCCGATGATCACGCGTCCGTGCAGATCAATGTCGCAAAGGTCGACGAGGAGGGTCGGGCAATCCCAGGGGAGTACATCACTTACGCACTGAGCGGCTATGTTAGGTCCCGGGGAGAATCCGACGACAGCCTGAACAGGCTTGCCCAGAACGATGGACTATTGAAGAATGTGTGGTCCTACAGTCGC
>SeqH
ATGGAGAACGATAAAGGGCAGCTGGTGGAACTTTACGTGCCGCGGAAGTGCTCTGCAACCAACCGCATCATTAAAGCTGATGATCACGCCAGCGTTCAGATTAATGTCGCTAAAGTCGACGAGGAGGGCCGGGCCATACCTGGCGAATACGTGACGTATGCCCTTTCAGGATACGTGCGGAGCCGGGGAGAAAGCGACGACTCTTTAAACAGGCTCGCCCAAAACGACGGGCTGTTGAAAAACGTGTGGAGCTATTCCCGG
>SeqI
ATGGAGAACGATAAGGGCCAGCTGGTAGAGTTGTACGTGCCAAGAAAGTGTTCAGCAACGAATAGAATCATTAAGGCAAAAGATCACGCCTCTGTACAGATCAGTATCGCGAAGGTGGATGAAGACGGCCGAGCCATAGCCGGAGAGAATATCACATACGCTTTGTCAGGGTATGTGAGAGGTAGGGGCGAAGCCGACGATAGTCTGAACCGTCTGGCCCAACAGGACGGTCTACTCAAGAACGTGTGGTCCTATTCAAGA
>SeqJ
ATGGAGAATGATAAGGGCCAACTCGTCGAGTTGTACGTGCCTCGTAAGTGCTCTGCCACTAACCGGATCATCAAAGCAAAGGATCACGGCTCAGTTCAGATAAATATCGCTCAGGTTGATGAGAATGGTCACGCCGTTCCCGGGGAATACATAACGTACGCACTCAGCGGATATGTTCGCGCAAGAGGCGAGGCCGACGACAGTATGAACCGTCTGGCGCAAAAGGATGGCTTGCTTAAGAATGTCTGGTCGTATAGCCGG
>SeqK
ATGGAAAACGAGGCTGGTCAACTGGTGGATCTCTATGTGCCCCGAAAGTGTAGCGCGACTAACCGGATCATCCAGGCAAAGGACCACGCTTCAGTCCAGATAAATGTATGCGCCGTTGACGCCGAGGGTAGACAAATCCCCGGCGAAAAGACCACGTACGCGATCTCCGGATTCGTTAGAAGCAAGGGGGAATCAGATGACTGTATCAACCGCTTGACCACTCAGGATGGACTTCTGGAGGGGGTGTGGAGTTACCAAAGG
>SeqL
ATGGAAAATGATGCAGGACAAGTTACTGAACTGTACATACCCCGGAAATGCAGTGCGACCAATCGCATGATTACGTCTAAGGACCACGCTAGTGTGCAACTGAACATAGGCCACCTGGATGCCAACGGACTTTATACCGGCCAGTTCACCACATTTGCCCTGTGTGGCTTCGTCCGCGCACAGGGGGATGCCGATTCCGGCGTGGATCGCCTGTGGCAGAAGAAGAAAGTGGAAGCCAAGCAGCAG
>SeqM
ATGCAAAATGAGGAGGGTCAGGTGACTGAACTGTACATCCCTAGAAAGTGCTCTGCTACAAACCGTCTTATCACCTCTAAGGATCATGCCTCAGTCCAGCTGAACATCGGGCACCTTGACGCAAACGGCCTCTATACTGGTCAGTTTACTACCTTCGCTCTGTGTGGATTTGTTCGGGCTCAGGGGGATGCCGACTCTGGAGTCGACAGGCTTTGGCAGAAGAAGAAGGTGGAGGCCAAGCAAAAACTTCGCGCG
>SeqN
AACATCGAGGGAAAGATCGTTGACCTTTACATACCTAGAAAATGTTCCGCAACTAAGAGGCTGATTCCTTCAAAAGAACACGGAGCAGTCCAAATCGATGTGGCCCTGGTCGACGACGAGGGCGTGGCAACTGGGCAAGTCGTGTCCTTCGCCATTTCTGGAGCCGTTAGGCAGAGAGGAGAGAGCGACGCATGCCTGAACAGGCTCTTTAATGAGAAGCAGATGCTGTCATTTAGTAAG

Insert codon usage table (codon usage database format) help

UUU 17.4(586747)  UCU 15.0(507382)  UAU 12.1(408578)  UGU 10.5(352664)
UUC 20.4(687969)  UCC 17.7(596425)  UAC 15.3(516505)  UGC 12.6(426761)
UUA  7.5(254407)  UCA 12.1(409879)  UAA  1.1( 35822)  UGA  1.6( 55514)
UUG 12.8(432797)  UCG  4.5(150335)  UAG  0.8( 27554)  UGG 13.3(447152)
	
CUU 13.1(440882)  CCU 17.5(589809)  CAU 10.8(363555)  CGU  4.6(155426)
CUC 19.7(664417)  CCC 20.0(675558)  CAC 15.1(509431)  CGC 10.6(357380)
CUA  7.1(240672)  CCA 16.9(569871)  CAA 12.1(408697)  CGA  6.2(208816)
CUG 39.9(1347830)  CCG  7.0(237033)  CAG 34.3(1157220)  CGG 11.6(390529)
	
AUU 15.8(532975)  ACU 13.0(438753)  AAU 16.7(563795)  AGU 12.1(408481)
AUC 20.9(705646)  ACC 19.0(641707)  AAC 19.0(642797)  AGC 19.5(656528)
AUA  7.4(249300)  ACA 15.0(504527)  AAA 24.1(812474)  AGA 11.9(402225)
AUG 22.0(744022)  ACG  6.1(205470)  AAG 32.0(1079579)  AGG 11.9(402146)
	
GUU 11.0(370035)  GCU 18.5(624602)  GAU 21.7(732533)  GGU 10.8(364282)
GUC 14.6(491325)  GCC 28.1(947810)  GAC 25.2(850343)  GGC 22.5(758251)
GUA  7.1(238697)  GCA 15.9(537665)  GAA 28.6(964323)  GGA 16.4(553492)
GUG 28.3(956245)  GCG  7.5(253270)  GAG 39.7(1340672)  GGG 16.6(558612)

Insert %G+C content (Optional) help

Upper (one-side) tolerance limit help

Confidence.
Population.

Choose the method help

Length of random sequences
Please, freely download the local version if more accurate analysis is required

Choose genetic code help

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For comments, suggestions or questions please send an e-mail to Pere Puigbo (puigboap AT ncbi.nlm.nih.gov) . Please put 'RCDI' as a subject.