Abstract
PRofile ALIgNEment (PRALINE) is a fully customizable multiple sequence alignment application. In addition to a number of available alignment strategies, PRALINE can integrate information from database homology searches to generate a homology-extended multiple alignment. PRALINE also provides a choice of seven different secondary structure prediction programs that can be used individually or in combination as a consensus for integrating structural information into the alignment process. The program can be used through two separate interfaces: one has been designed to cater to more advanced needs of researchers in the field, and the other for standard construction of high confidence alignments. The web-based output is designed to facilitate the comprehensive visualization of the generated alignments by means of five default colour schemes based on: residue type, position conservation, position reliability, residue hydrophobicity and secondary structure, depending on the options set. A user can also define a custom colour scheme by selecting which colour will represent one or more amino acids in the alignment. All generated alignments are also made available in the PDF format for easy figure generation for publications. The grouping of sequences, on which the alignment is based, can also be visualized as a dendrogram. PRALINE is available at http://ibivu.cs.vu.nl/programs/pralinewww/.
Keywords
Multiple sequence alignmentSequence alignmentToolboxHomology (biology)Structural alignmentBiologyComputer scienceVisualizationData miningComputational biologyGeneticsPeptide sequenceAmino acidProgramming language
MeSH Terms
Computer GraphicsCytochrome P-450 Enzyme SystemDatabasesProteinInternetModelsMolecularProtein StructureSecondarySequence AlignmentSequence HomologyAmino AcidSoftwareSystems IntegrationUser-Computer Interface
Affiliated Institutions
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Publication Info
- Year
- 2005
- Type
- article
- Volume
- 33
- Issue
- Web Server
- Pages
- W289-W294
- Citations
- 506
- Access
- Closed
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Cite This
V. A. Simossis,
Jaap Heringa
(2005).
PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information.
Nucleic Acids Research
, 33
(Web Server)
, W289-W294.
https://doi.org/10.1093/nar/gki390
Identifiers
- DOI
- 10.1093/nar/gki390
- PMID
- 15980472
- PMCID
- PMC1160151