pal2nal -nogap -nomismatch options not working
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19 months ago
pkfsantos • 0

Hi All,

I am trying to generate a codon-aware nucleotide alignment using the protein alignment (output from Orthofinder) and their respective nucleotide sequence.

For that I am using pal2nal with the following command:

perl pal2nal.pl pep_algn.fa nucl_seq.fa -nogap -nomismatch -output palm > nucl_algn.fa

That works for 4 out of the 36 alignments that I am testing. For all the other sequences I get this error message:

#---  ERROR: inconsistency between the following pep and nuc seqs  ---#

I get the same error message if I run it on the pal2nal website.

Here is one example of sequences resulting in this error message:

>Edil_01564-mRNA
MEQLGEGQAVVVGSAGGTVQVVQMGQGGQAMMLPQAIQVAAPNGQIQVVPVSSLTSTGQQ
IVIQQPQTPQIIQTPDGQTYIYQPVQLEGQVQQAQPTVININGNLMQIAGTTSQTTTTAA
TTTPVQPLASPTATASQAGNVVMMVPGNSGQTQFQRVALPNAEVFEEEPLVNAKQYRRIL
KRRQARAKLEAEGKIPKERPKYLHESRHRHAMNRIRGEGGRFHSGQVKKRNRINENAMIT
QHITTSTSTNTVRTIAIAAANVGVQYHDTDNMASTIVIEKQGIPLQDMISEDDIVTSNNC
LM

>Edil_01564-mRNA
ATGGAACAACTGGGAGAAGGGCAGGCGGTTGTGGTTGGTAGTGCCGGAGGAACCGTCCAAGTTGTTCAGATGGGCCAAGGAGGCCAAGCAATGATGTTGCCACAAGCTATACAAGTTGCAGCACCAAATGGACAAATAC
AAGTTGTTCCTGTATCTAGCTTAACCAGTACAGGTCAACAAATTGTAATTCAACAACCGCAAACACCTCAAATAATCCAAACTCCAGATGGACAAACTTATATTTATCAACCAGTTCAGTTGGAAGGTCAAGTTCAACA
AGCACAACCAACAGTAATTAATATCAATGGGAATCTTATGCAAATTGCTGGAACTACGTCACAAACCACAACCACAGCAGCAACCACAACACCAGTACAACCATTAGCGAGTCCTACAGCTACAGCGTCTCAGGCAGGA
AATGTTGTCATGATGGTGCCAGGAAATAGCGGGCAGACACAATTTCAAAGGGTAGCATTGCCAAATGCAGAAGTTTTTGAAGAAGAACCTTTATAAGTAAATGCTAAACAATATAGACGTATATTAAAACGCCGTCAAG
CTCGGGCAAAATTAGAAGCTGAAGGAAAAATACCTAAGGAAAGACCTAAATACCTTCATGAATCGCGTCATCGGCATGCCATGAACAGAATTCGGGGTGAAGGTGGTCGTTTTCATTCTGGTCAAGTAAAAAAGCGAAA
TAGAATAAACGAAAACGCCATGATTACCCAGCACATCACAACTTCGACCAGCACCAATACCGTTCGTACTATAGCAATAGCAGCAGCAAATGTAGGTGTTCAGTATCATGACACAGATAATATGGCCTCTACAATTGTC
ATCGAAAAACAAGGTATTCCTCTTCAAGATATGATCTCTGAAGACGATATCGTTACCTCAAACAATTGTTTAATG

I run blastx to see the inconsistency and it seems to be one stop codon that was removed in the protein alignment but was kept in the nucleotide sequence. I understand that pal2nal is able to deal with gaps and mismatches between the protein and nucleotide sequences. But even though I include these options in the command line, it doesn't apply.

Does anyone have had similar issues? I really appreciate any thoughts on that.

Thank you,
Priscila

pal2nal • 1.2k views
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Hi, did you end up solving this? I am running into the same issue.

Marie

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I am running into the same issue! How did you solve this problem? I will be very grateful!

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I just write a perl script by myself, and integrating the pal2nal.pl, parseFastaIntoAXT.pl, and Kaks_calculator.pl together.

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