PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information

By Victor A. Simossis, Jaap Heringa. Nucleic Acids Res., 2005

523 citations recorded by the source corpus.

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 .

Subfields: Materials Chemistry, Molecular Biology, Pharmacology

View Paper: https://www.semanticscholar.org/paper/1faef82b3c027c9285763f51aea903d140221fdc

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Erik S. Wright

Citations in the corpus

PROMALS: towards accurate multiple sequence alignments of distantly related proteins (2007, background): “, 2000), predicted secondary structure (Simossis and Heringa, 2005; Zhou and Zhou, 2005), and known 3D structures (O’Sullivan et al.”
Multiple sequence alignment. (2006, unknown): “Finally, CONTRAlign [30] is a newly developed experimental protein alignment tool that uses discriminative learning techniques recently introduced in the machine learning literature.”
DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment (2015, background): “Those programs that have integrated secondary structure predictions into alignment have shown noteworthy gains in Q-score [27 – 31].”
The extracellular contractile injection system is enriched in environmental microbes and associates with numerous toxins (2020, methodology): “We used two cluster representatives for structural prediction in Phyre2 75 , and secondary structure alignment using Praline 76,77 .”
Deciphering key features in protein structures with the new ENDscript server (2014, unknown): “Alscript (10), BoxShade or PRALINE (11)).”
Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee (2006, background): “To the best of our knowledge, only six algorithms have been designed that are able to make use of secondary (6,7) or tertiary (8–10) structure information.”