For better experience, turn on JavaScript!



Praline is a multiple sequence alignment program that provodes several different alignment strategies, e.g, integration of structural information in the alignment process. It also provides a comprehensive visualization of the multiple sequence alignments. SOAP service is available.


Structure prediction; Protein secondary structure; Sequence analysis; Protein folds and structural domains; Nucleic acid structure analysis


  • Operation: Sequence similarity search; RNA secondary structure prediction; Protein secondary structure prediction; Multiple sequence alignment
  • Input: Protein sequences in FASTA format
  • Output: -
  • Software interface: Web user interface
  • Language: -
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: Not stated
  • Cost: Free
  • Version name: -
  • Credit: -
  • Contact: bioinf-l _at_
  • Collection: -


Simossis VA, Heringa J "PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information." Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W289-94.
PMID: 15980472
PMCID: PMC1160151

Simossis VA1, Heringa J "The PRALINE online server: optimising progressive multiple alignment on the web." Comput Biol Chem. 2003 Oct;27(4-5):511-9
PMID: 14642759

Download and documentation

If you find errors, please report here.