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The PRALINE online server: optimising progressive multiple alignment on the web by V.A. Simossis; J. Heringa is a Biochemistry, Genetics and Molecular Biology article available to read on EtoBox.

What is The PRALINE online server: optimising progressive multiple alignment on the web about?

We introduce the online server for PRALINE (http://ibium.cs.vu.nl/programs/pralinewww/), an iterative versatile progressive multiple sequence alignment (MSA) tool. PRALINE provides various MSA optimisation strategies including weighted global and local profile pre-processing, secondary structure-guided alignment and a reliability measure for aligned individual residue positions. The latter can also be used to optimise the alignment when the profile pre-processing strategies are iterated. In addition, we have modelled the server output to enable comprehensive visualisation of the generated alignment and easy figure generation for publications. The alignment is represented in five default colour schemes based on: residue type, position conservation, position reliability, residue hydrophobicity and secondary structure; depending on the options set. We have also implemented a custom colour scheme that allows the user to select which colour will represent one or more amino acids in the alignment. The grouping of sequences, on which the alignment is based, can also be visualised as a dendrogram. The PRALINE algorithm is designed to work more as a toolkit for MSA rather than a one step pr

Who reads The PRALINE online server: optimising progressive multiple alignment on the web?

Author

V.A. Simossis; J. Heringa

Publisher

Elsevier Science; Elsevier ; Elsevier Ltd.; Elsevier BV (ISSN 1476-9271)

Published

2003

Language

EN

Field

Biochemistry, Genetics and Molecular Biology (Life Sciences)