PROTEIN ALIGNMENT USING ONE REFERENCE SET

Use this option to calculate the Codon Adaptation Index (CAI) from protein alignment that has been translated to a DNA alignment using a unique codon usage table as a reference.

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Insert your protein alignment

SeqA         MQNDAGEFVDLYVPRKCSASNRIIAAKDHASIQMNVAEVDRTTGRFN-GQFKTYGICGAI
SeqB         MQNDAGEFVDLYVPRKCSASNRIIAAKDHASIQMNVAEVDRSTGRFN-GQFKTYGICGAI
SeqC         MQNDAGEFVDLYVPRKCSASNRIIGAKDHASIQMNVAEVDKVTGRFN-GQFKTYAICGAI
SeqD         MENDAGENVDLYVPRKCSASNRIIHAKDHASVQLSIVDVDPETGRQT-DGSKTYAICGEI
SeqE         MQNDAGQTVELYVPRKCSSSNRIIGPKDHASVQIDFVDVDPETGRMIPGKSTRYAICGAI
SeqF         MQNASGRIVDLYVPRKCSVTNRLISAKDHASVQLNIAKVDPDTGRMVPGEHLTVALTGSI
SeqG         MENDKGQLVELYVPRKCSATNRIIKADDHASVQINVAKVD-EEGRAIPGEYITYALSGYV
SeqH         MENDKGQLVELYVPRKCSATNRIIKADDHASVQINVAKVD-EEGRAIPGEYVTYALSGYV
SeqI         MENDKGQLVELYVPRKCSATNRIIKAKDHASVQISIAKVD-EDGRAIAGENITYALSGYV
SeqJ         MENDKGQLVELYVPRKCSATNRIIKAKDHGSVQINIAQVD-ENGHAVPGEYITYALSGYV
SeqK         MENEAGQLVDLYVPRKCSATNRIIQAKDHASVQINVCAVD-AEGRQIPGEKTTYAISGFV
SeqL         MENDAGQVTELYIPRKCSATNRMITSKDHASVQLNIGHLD-ANG-LYTGQFTTFALCGFV
SeqM         MQNEEGQVTELYIPRKCSATNRLITSKDHASVQLNIGHLD-ANG-LYTGQFTTFALCGFV
SeqN         --NIEGKIVDLYIPRKCSATKRLIPSKEHGAVQIDVALVD-DEG-VATGQVVSFAISGAV

SeqA         RRMGESDDSILRLAKAD---------GIVSKNF-----------
SeqB         RRMGESDDSILRLAKAD---------GIVSKNF-----------
SeqC         RRMGESDDSILRLAKAD---------GIVSKNF-----------
SeqD         RRMGESDDCIVRLAKKD---------GIITKNF-----------
SeqE         RRMGESDDAILRLAQKD---------GLVPRDDVKSN-------
SeqF         RRLGLSDQAVFRLAKEKGALDDLRGGGAVGVGSGASGGAEERTD
SeqG         RSRGESDDSLNRLAQND---------GLL-KNVWSYSR------
SeqH         RSRGESDDSLNRLAQND---------GLL-KNVWSYSR------
SeqI         RGRGEADDSLNRLAQQD---------GLL-KNVWSYSR------
SeqJ         RARGEADDSMNRLAQKD---------GLL-KNVWSYSR------
SeqK         RSKGESDDCINRLTTQD---------GLL-EGVWSYQR------
SeqL         RAQGDADSGVDRLWQK--------------KKVEAKQQ------
SeqM         RAQGDADSGVDRLWQK--------------KKVEAKQKLRA---
SeqN         RQRGESDACLNRLFNE--------------KQMLSFSK------

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)

*Choose genetic code

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