E-CAI (EXPECTED CAI CALCULATION)

The E-CAI server is a web-application and an executable program that calculates the expected value of the Codon Adaptation Index (CAI) for a set of query sequences by generating random sequences with similar G+C content and amino acid composition to the input. This expected CAI therefore provides a direct threshold value for discerning whether the differences in the CAI 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.

HOW TO CITE: Puigbo P, Bravo IG and Garcia-Vallve S. (2008) E-CAI: a novel server to estimate an expected value of Codon Adaptation Index (eCAI). BMC Bioinformatics, 9:65.

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Insert your sequences in FASTA format

>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)

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)

Upper (one-side) tolerance limit help

Confidence.
Population.

Choose the method help

Choose genetic code

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TUTORIAL FAQs Local Version

For comments, suggestions or questions please send an e-mail to Pere Puigbo or Santi Garcia-Vallve (santi.garcia-vallve AT urv.cat). Please put 'E-CAI' as a subject.

This Server has been financied by:

(Ref. BIO2003-07672)