Why Ks value is NA in KaKs calculator

Question

[Laura_zz]

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?

[lieven.sterck]

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?

Answer 1

[fznajar]

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.