PAL2NAL

Convert a protein sequence alignment and the corresponding DNA sequences into a codon alignment.

PAL2NAL assigns the corresponding codon to every aligned residue, even where the DNA sequence has mismatches with the protein, or carries UTRs and a polyA tail. It can also deal with frame shifts in the input alignment, which makes it suitable for the analysis of pseudogenes.

You can also install PAL2NAL from the source code and run it locally as a command-line program, which has none of the size and time limits this server applies. The last Perl release, pal2nal.v14.tar.gz (December 2011), is still served at its original address for the pipelines that fetch it, but it is no longer maintained.

Protein alignment

CLUSTAL or FASTA format; the format is detected automatically. In a CLUSTAL alignment you can select specific positions by putting # under them, for use with the filter below.

or upload a file

Marking stop codons and frame shifts

An in-frame stop codon is written * or _, so NGDLP*PQLKN and NGDLP_PQLKN are equivalent.

A frame shift is written as a digit in place of a residue. The digit says how many nucleotides the column accounts for:

`HCDGE` `HC1GE`	only 1 nucleotide residue
`HCDGE` `HC2GE`	only 2 nucleotide residues
`ND-TY` `ND1TY`	1 nucleotide residue inserted
`ND-TY` `ND2TY`	2 nucleotide residues inserted
`EREQK` `EK4QK`	1 nucleotide residue inserted

DNA or mRNA sequences

FASTA format. Sequences are matched to the alignment by ID when the IDs correspond, and by order otherwise.

>BC0700280  dihydrofolate reductase (human)
TGTAACGAGC GGGCTCGGAG GTCCTCCCGC TGCTGTCATG GTTGGTTCGC TAAACTGCAT
CGTCGCTGTG TCCCAGAACA TGGGCATCGG CAAGAACGGG GACCTGCCCT GGCCACCGCT
CAGGAATGAA TTCAGATATT TCCAGAGAAT GACCACAACC TCTTCAGTAG AAGGTAAACA
GAATCTGGTG ATTATGGGTA AGAAGACCTG GTTCTCCATT CCTGAGAAGA ATCGACCTTT
AAAGGGTAGA ATTAATTTAG TTCTCAGCAG AGAACTCAAG GAACCTCCAC AAGGAGCTCA
TTTTCTTTCC AGAAGTCTAG ATGATGCCTT AAAACTTACT GAACAACCAG AATTAGCAAA
TAAAGTAGAC ATGCTCTGGA TAGTTGGTGG CAGTTCTGTT TATAAGGAAG CCATGAATCA
CCCAGGCCAT CTTAAACTAT TTGTGACAAG GATCATGCAA GACTTTGAAA GTGACACGTT
TTTTCCAGAA ATTGATTTGG AGAAATATAA ACTTCTGCCA GAATACCCAG GTGTTCTCTC
TGATGTCCAG GAGGAGAAAG GCATTAAGTA CAAATTTGAA GTATATGAGA AGAATGATTA
ATATGAAGGT GTTTTCTAGT TTAAGTTGTT CCCCCTCCCT CTGAAAAAAG TATGTATTTT
TACATTAGAA AAGGTTTTTT GTTGACTTTA GATCTATAAT TATTTCTAAG CAACTTGTTT
TTATTCCCCA CTACTCTTGT CTCTATCAGA TACCATTTAT GAGACATTCT TGCTATAACT
AAGTGCTTCT CCAAGACCCC AACTGAGTCC CCAGCACCTG CTACAGTGAG CTGCCATTCC
ACACCCATCA CATGTGGCAC TCTTGCCAGT CCTTGACATT GTCGGGCTTT TCACATGTTG
GTAATATTTA TTAAAGATGA AGATCCACAT ACCCTTCAAA AAAAAAAAAA AAAAAAAAAA
AAAAAAA
>pseudogene  dihydrofolate reductase pseudogene (human)
CTAAACTGCA TTGTCAATGA TTCCCAGAAG ATGGGCATCA TCAGGAATGG GGACCTGCCC
TGACCTCAGC TCAAAAATAA ATTCGATTCC AAAGAATGAC CACACCCTCT TCAGCAGAGG
GTAAAGAAAA TTTAGTATTT TTAATTAGGA AGAACTGGTT CTCGATTACT GAGAAGAATC
AACCTTTAAA GTATATAATT AATTTAGTTG TCAGTAGAGA ATCCAAGGAA CCACCGCAAA
GACCTCCTTT TCTTGACTAA AGTCTGGGTG ATGCCTTAAA ACGTATTGAG CAACTAAAAT
TAGCAAATAA ACAAGACGTG TTTTTTACAG TGGGAGGCAG TTCTGTTTAT AAGGAATCCA
TGAATTGAGA CCATTTTAAA CTATTTGTGA CATGGATCAT GCAGGACTTT CAAAGTGACA
CGTTTTTTTC CCCTAGAAGG TGATTTAGAG AAATATAAAC TTCTCCCAGA ATACCCACAA
GGTGTTGTCT CTGATGTGGA GGAGGAGAAA GGCATTAAGT ACAAATTTGA AGTATATGAA
AAGAATGAT

or upload a file

Options

Codon table

Tables 34–37 are not NCBI assignments; the numbering is Wikipedia's.

Output format

Filters Remove gaps and in-frame stop codons
Remove mismatched codons
Use only selected (#) positions

Matching Convert partial matches

Where a peptide and its DNA do not correspond – a retained intron, an indel, a CDS truncated at either end – keep the codons that can be matched and gap the residues that cannot, instead of stopping the whole conversion. Input that converts without this option converts identically with it.

load an example · an example with an intron, which needs partial matching