Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments.

Mikita Suyama1, David Torrents, Peer Bork

  • 1European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany.

Nucleic Acids Research
|July 18, 2006
PubMed
Summary

PAL2NAL is a web server that generates multiple codon alignments from protein sequences. This tool aids evolutionary analyses, including selective constraint identification and phylogenetic studies, even with imperfect DNA inputs.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

EpiATLAS - a reference for human epigenomic research.

bioRxiv : the preprint server for biology·2026
Same author

Development of a robust method to derive human trophoblast stem cells from late-gestation placentas and its application to preeclampsia.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same author

Multimodal data analysis reveals asynchronous aging dynamics across female reproductive organs.

Nature aging·2026
Same author

Medullary cavity expansion is mediated by distinct cell populations during fetal bone development.

Nature communications·2026
Same author

A hierarchical Rorc(γt) cis-regulatory cascade orchestrates differentiation of RORγt⁺ innate immune cells.

Immunity·2026
Same author

Screening the Human Proteome for Peptides Targeting the Acidic Environment of Tumor Tissues.

Chemical & pharmaceutical bulletin·2026

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Evolutionary Genetics

Background:

  • Multiple codon alignments are crucial for evolutionary analyses of coding DNA.
  • Existing tools often struggle with DNA sequences containing mismatches, untranslated regions, or polyA tails.
  • Analysis of pseudogenes requires handling frame shifts and in-frame stop codons.

Purpose of the Study:

  • To introduce PAL2NAL, a novel web server for constructing multiple codon alignments.
  • To provide a robust tool capable of handling complex DNA sequence variations.
  • To facilitate detailed evolutionary analyses of coding DNA, including pseudogenes.

Main Methods:

  • The PAL2NAL server accepts aligned protein sequences and corresponding DNA sequences as input.

Related Experiment Videos

  • It constructs codon alignments, accommodating mismatches, untranslated regions, and polyA tails.
  • The server supports analysis of frame shifts and in-frame stop codons, and allows user-specified subregion analysis.

    • Main Results:

    • PAL2NAL successfully generates multiple codon alignments from protein sequence alignments and DNA sequences.
    • The server demonstrates enhanced capability in handling DNA sequences with imperfections compared to existing methods.
    • It is suitable for analyzing pseudogenes and specific functional regions within genes.

    Conclusions:

    • PAL2NAL offers a versatile and robust solution for multiple codon alignment.
    • Its ability to handle sequence variations and pseudogenes expands the scope of evolutionary DNA analysis.
    • The tool supports focused studies on specific gene regions, enhancing phylogenetic and selective constraint analyses.