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Why Ks value is NA in KaKs calculator

My sequence is :

>AAA
ATGGTGGGGCAGACCATGATGCGCATCGTGCGGCCCTGCTTCAAGCCCTCGCTGCCCGACGGCGCGCAGGTCGTCGCCGCCGGGGGCGGCGGCACCAGGGAGGGCCTGCTCTGGTACAGGGACGCCGGCCGCCACGCCTGCGGCGACTTCTCCATGGCCGTCGTGCAGGCCAACCAGCTGCTCGAGGACGCCAGCCAGCTCGAGGCCGGGCCCCTCGTCGCCGCCGACGGGCCCTGCGCCACCTTCGTCGGCGTCTACGACGGCCACGGCGGGCCCGAGACCGCCCGCTTCGTCGCCGATAACCTCTTCCACCACCTCAAGAAGTTTGCGACGGAACAACAGACAGTCTCGGCCGACGTGATACGCCGATCCTACGCTGCCACGGAGGAGGGCTTTCTGAACCTTGTGAGGAAGCAGTGGCTCATCAAGCCGCAGATCGCCTCGGTCGGTACATGTTGTTTGGTTGGCATTATCAACGAAGGTGTTCTGTACATAGCAAACGCCGGCGACTCCCGTGCTGTCCTCGGGAGAGTCGAGCGGGGCGCCAAAGACATTAAGGCAGTTCAGCTCTCGTCCGAGCATAACGCGAGCTTTCAGGAGGTAAGGGATGAGCTAAGACAGATGCACCCGGACGACCCCCGGATCGTGGTCCTCAAGCACAATGTTTGGCGCGTCAAGGGCATTATTCAGGTTTCCAGAACGATCGGTGACGCCTACCTAAAAAGTTCGGAGTTTAACCGCGAGCCTCTTCTGGCCCGGTTCCGTATTCCAGGGCCCTTCCATAAACCGATTCTTTGTCCGGAACCATCCATAGAAGAACACAGACTGTGCGCAGAAGATCAGTTTGTTATATTTGCGTCAGATGGACTATGGGAGCACTTGAGCAATCAGGAAGCTGTGGATATAGTTCATTGTTCGCCTCGGAATGGCATTGCGAGACGACTAATAAAAGCAGCTCTGCGGGAGGCGGCAAAGAAGAGAGAAATGAGATACTCAGACTTGAAGAAGATCGACCGCGGGGTCAGGAGGCACTTCCACGATGATATTACTGTTGTGGTATTATTCATGGACCCTGCGCTTGTCAGCAGGAGGCTCTACGGTGGGCCGTTGCTTTCGCTAAGGGGTGGTGGCAGCACGCCAACGTTTGCACAGAAATGC
ATGAATGACACTAATCCCTCGGTTCCATCTTTCAGGAGGCAGATTCTGCTCGGTCTCTCTTGGTTTAGGCCAACGCAGATGGTTGATCCTGACGATCTTCGGAGGGCGATCGGTCTTCCTGTTACTGCTTCGCTGGGCCCTGTTGGTCCCCTCCTCCGGCAACTCCATGAGGGGGTCAGTGAGGATGAGATTCAGAGGCTCACGGTGCATTTCGATGGATTATGCGTCTCCCTCATGCATCAGTCAGAGGTGGAGAAACCTAGCTTCGCCGCCAAGTGCTGGATGAGTGAGGTCCGGGAACTTTGCTACGACAGCAAAAACTACTTCGACGATGCCCCGTTTATTTCCAAGCAAGACGACGACGATGATGATGCCCAGCTCACTCCAGAAGAGAAGCAAGAAAATGCCCAGTTCGAGTTCAAGATGATCGAGGCTCGCGCGGAGCATGCGTATGGGAGAAGGGGAAGGTACGGATTCGACCAGAAAAGCGTCAATAAGACCACTAAGATTCCATCAACAGGACGCCGGCTCCCAGTTCTCCATCCGGAACTAATTGATCGTTGCCGAATGGATCAACTTGACACCTTGCTTCGTAAGGATGAGGAGCAGCAGCTCAAGGTCGTATCTCTGGTAGGATTTGAGGGTGTCGGTAAAACCACACTTGCCAAGAGGTTATACCACCATAGAGGTGGGCAGTTCAACTGCCGGGCTTTTGTGCGGGTGTCTCCCAACCCGGACATGAGGAGGCTTCTAACCACCATATTCACCCAGATTCAATTGCCGACCTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTGGTACTGTCTCTCAGCCTGCTTGCTGCTTGGATGCGCAGGCCCTCATCATAAATATTGCAAAATATCTCCAATCAAGAAGGTACTTAATCATAATTGATGACTTATGGAGTACTTCAGCATGGGATGTTATTAGGCGTGCTTTTCCTGATGGTGATTGTCACAGCAGAATTATAACAACCACCCAATTCGGGGATGTAGCATCGGCATGTTGTAGTTATCAGTCAAAGTACGTATTTCATATGGAACCTCTAAAATATGATCAATCACGAAAATTGTTTTTCAGTATAGTGTTTGGCTCTGAAGATAAAGTCAGTTTTCCTGAGGATTTCAGAGAAGTCTCATCTGAGATTGTCAAGAAATGTGGTGGTTTACCATTATCAATTATAAATATAGCCAGCTTGTTGCCAACAGAAGAAAGCGAAATAAACCTCCAGCAATGGATGGACATTCGAGATTATATGCCTTCCACTATGAGGACAAATCCTACGCCCGAAGGGATAAAACAAGTTCTAAACCTTGTCTACAATAATCTTTCCCCTGAACTGAAGACATGCTTGCTGTATCTTGTTGTGAATCCAGAGGGCTACATGGTGAGTAAGGATGATTTGGTGAAGCAATGGGTAATTGAAGGTTTTATACGGGAAGGACAAAACAAAGAGGAAATTGCAGGGGGTTATTTTGATGAGCTTGTCAGGAGAGGCATGATCCAGGCTGTAGACATCAATTACCGAGGGGTGCTGTCATGTACACTTCACCACATGGTACATGATCTTATTGTGAAGAAATCCATTGAGGAAAATTTCATAGTTATCCAGGACTGTTTTCAATCAGCTATAGGTCTTCCTGACAAAGTTCGTCGTCTGTCTGTCCAATTCGGTGGTGCAAGGAGCGCAAATATACCGATGGGAGTCATGATGTCTGAAGTTCGATCACTTGCATTTTTTGGATTCTATGGATGCACGGACTTCATTGAGGAGTGTAAGCTTCTTCGAGTTCTAATTCTCCATGTGTGGGCTGATGAAGATAAAGTGCCTTTTGACCTCTCTGAAATTATTAGTAAACTACTTCCATTGAGATATGTGAAGATTGCATGTAATATCGCTGTCAAACTTCCAGCCGAGATTCAAGTTCTGCAATTCCTGGAGATACTGGAAGTGGATACACCAGTAGTTGCTATCCCATCGGATATTGGAGGACTCAGCAGGCTGTCCAGTCTAAAGATTGCAGTTACAGAGCTATTGAGGGAAGACATTTGTATCCTCCAAAAATTGGCAGCCCTCACTACTCTTTCAGTGGACGTGAAGACATCACCCACTGAATGGATCGTCTTTGGAAAGGGAGGATTCTTGGTCCTCACTTTCTTCACATTCAGGTGCAGTGCACCTCGTCTGCTAATTGAAGATAGTGCAATACCTAAATGCGAGAAGCTACACCTATGTTTAAATGGCCACGAAGCATCTCCTCGAGATGGTAAGAAGCCTATCACCATCGAGCACTTGGCAAGCCTTAAAGAGATATCTGTAAAAATTTGGGGTGCAGTTGCTAACAAGGGGTCCGCCTTGACGAATGTTATTACCAATGATGCAAGAAATCCTATTCCTAACGTTCAATTGATGGGTGATACCAGTGGTGTAGAAGTCCACATGATCTTCGACCTCAACGATGGTGATTATGCTGAATTCATCCGCCTCCTTATTGGCGTGCTCGTGAGGTACGACGACGGTGAACACATCCAAGGGTATCCTCCTGTTCTGGGTAAGCAACTGTTCCCGAAAGAGCCAAACAGGTGGATGCGCATCAAGCTAGTGGCCGGCATGACTGAAACAATCCTTGCTGTTCGGGATGACAATCTGAACCTCATTGGCTTCCAGGCTAAAAACGGAAGGTGGTACGAGTTGGGGTTCGCAGGGAGGAGCACACGAATGCTTCCTGGATCCACCTTTTTAGACTGCGATTGTGACTATACAGACTTGCTACAGGTAAAAGCTACCTGTCTGGAAGAAAGAAACCGACTAGTCAGGGAAGAAATGGTGAAGATAGAGCTAGGCAAGACCTCCTCAATTGAAGCCGTGGGTATTCTCTCGGGCTACAATAATAAAACGGAAGGTGTGGCAGCTGATCGAGACACCAGGCGGGCACTGGTGCGCCTAATGCTCATGTTGTGCGAGGCCACGAGGATGACCCCATTCTTTGACACCGTGCTGGCTAGCTGGAGCGACACACAAGGAGGGAATAGCCATATCTTGAGAGAGGACCAGGCAATGTACGTTTGGTACTGGGGAAAAATGTCGGCCGTGCTGCTGGAGTGGGAGGCAACAGGTTATAAGAGTTGGGGACCAAATGAGACCACCGCGATGCTGGCCAATGAAATCAATGTCAAATCTGCACAAGAGGCACTCGCTGTCGTCAAGGTGCTTCTCAACACACCCGTCGCCCCCAACAACACTTGCACCAGAGGAGGCCGACCTCTTGTGGAGGTGTTTACCATGCGTGCTGACTCCGGTGTTGTTGACACCATTTCGGTTTTTGACGGGAGACGTGGCCAGACCATATACAGACACCATGCTAGCCCCACTCCTATCCACCACTTTTGGTCTTCGTCTCAAGGTCCTAACGATTTGGTACTCACTGGACCATATAGAGCCATCTCAGCGGAGGGCAGCTTCGCCATCCAAGTCGACAGCATCATCTCCAGGACAGACGCCTCTGACGAACCTAGTAAAGTCAGTGCTGACATGTCCTGGGATTGCTACTCCGGTGAAGCCTCCATGTACAACAAGGTCTTGACCAACCGCATCGCCACAGACGACAAAGGCCAACTTGCAGAAGTGGCCTATGCTGTGTTCAGTGACGCCGTGGAGGTCACCGTCCAAATAAAGGTGACTAGAGTTGACCCCGCCGACGTTTACGGTAAAATCACCGCGCACAACCAGCACTACGGCAGCAACAGCATACTGCTCTTCAGCCGTACAGATTGGGATTTCCTTGCAACAAAGGAGGAAAAGAGGCAAGGAAGAAGGCGTGCAAAACTGAGGGCAAGTGGAACTTCCAATTGCTGGATTCCACTTACGCGATCCGTCGTTGCGGTGCCATTAGGCTCGCCGCTTGAGATAAGGGTCAATTTGTATGCATGTCCATCCGAATATGGGCTTACTGATTATTTCAAGGAGGATATAGATTTTTCTCTCATAGATCAGCATGTGGGGCAAATCAAAAGGCACCATGTGGTGGTTCGAGTGACCTCGCTGGACATCTGCACTCTCCCGGAACAAAGTCACACAACACTGCCTACGCTCGCCATGACCTGGGTTCCAGGGGTGACAAGTATGAGGACGGGGGCAGGAATGCCCATCGAGCAGCCTGCACATGTGTATATGGACTTCAACTGTGGCAGTGGTAAGTACAGTGCATTCATGGACGACTTGTGTGAAAAGCTTGCGGAGCACCCGGGCAAAGCTGCTGTCCATGGGCGGCCTGTCCTCGCCAGGCAGCGGCGTGGAAAGCCAACGAGGCTGTTTATGATCAGGCTAGCGGGTGACAGAGATTATGAATGGGTAACTCTGGCCGTTCGGGACGACAACTTGTGCCTCGTTGGCTTCCAAACTCCGGACGGGAGGTGGCACGAGTTCGGCTCCGGCTCCATAACTTGTCTCCAAGAGTCCACCTTTTTAGGGTCCAATGGAAGCTATGATAGCTTATTAGGTGAATCTGGAGACCGGTGGCAAGAGCTGAAGCTGGGCAGGAAGTCCGCAACAGATGCCATAGGAAAGCTCTCGGCGTACGAGGACCGAGTGGGCGTAGTAGTTGATCAAGACACCAAAGTGGATTTGGCTCGCCTGATGGTCATGATATGCGAGGCCGCACGGTTGGCAGAAATCTACGACATGGTGAAGAAAGGATGGGAAGACGGAATCTGTATCACCGACCGGCAGGTACAGCACATAGATAACTGGGACAATATTTCTCGCGTTCTGCTTGGCAGAAGAAGGAGAGTCAGAAACATAGGTTTGAAGAAGGAAGACGACGCGGCAGCTGTAGTGAAGATGGTGCTTAACCCTTTCCGTCCCCTTGTGGAGGTGTTTGGCCTGCGTGCTTACCCTAGTTTCAGTGGCACCATCTCCGCCGTGGACGACAAAGGAAGCAAGGTCGTCATTTACAACAAGGACCCTCAAGCCAAACGAGATGATACTCCGTCCTCTCAGACGCAAACTCAGAGTAATATCGATTGTCACCACAAAGAAGCACAGGAGGATTTGCCACCTGCTGTAACGTACAGACCCATCTCAGCTGACGGGGAGTTCTACATTCAAGTCAGTGGCAATTCCACCACACATACCTCCCGTCTCACCTTGGTATGGGATGGTCATTCCGATAAAGCTGCGTACAACATCATCAACACACACCAAATCAGCATAGGCAGCTCCAAAGCTGAACTAACGTATGCGGTGCTCCACGATGCCGTGGAGGCCACCGTGAAGGTCCAGCTGAATCTCAAGGAACCCGAAGAAGCTGGCACCGTCACCGGCGTGTACGGTGAAATCACCGCGACCAACCAGCACTACAAGAACAAGAGCATCCTGCTCTTCAGCCATCCAAAGGAACAGGCAGTAAAACCCGAGGTCAATGCCTCGGATGCCGTTTCAATTTCACTCAAGTTGATGAGGGGTTTCATTGTGGCGTCACTTGAGCGCTTGCTTGTGATAAAGGTTAGCTTGCGTGCTGTGTGCTCCAGCTATGAGGAACCCATATGCTTCGAGCAAGAAGTGAGTTTCGACCCCAATATGGGTACCGCGCAAACAGCGAAGATCGATGCACCCACTATGGAGGCTCAAGTGATGTTCATCACCAACGAGCGAAATGCGCCCAGCCAGGGAAGGGTAAAGCAATGGCGCCGGCGACCACGCGCGAGTGCCGCAATACTCCCCAACACTACTACTGCGGGA

In the KaKs calculator, I use the NG method and get the NA of the ks value. I don't know what problems they have. What should I do?

kaks software error gene
• 2,365 views • link
updated by fznajar • fznajar • written by Laura_zz • Laura_zz

at first sight there are a few things going on here:

  • for KaKs analysis you need two sequences (can we assume the ones you posted are actually two sequences)
  • the sequence needs to be correctly aligned, for Ks analysis that should even be codon-aware alignment
  • normally you would expect the sequences to be of comparable length (Ks analysis only makes sense between homologous sequences)

Can you check these points first?

• 0 views • link
written by lieven.sterck lieven.sterck

1 answer

If the nucleotide and amino acid sequence are correctly aligned, this could be due to a SNP that results in the generation of a stop codon. Hence you are getting a truncated protein.

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written by fznajar • fznajar

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