Tailor-made multiple sequence alignments using the PRALINE 2 alignment toolkit

Research output: Contribution to JournalArticleAcademicpeer-review

Abstract

SUMMARY: PRALINE 2 is a toolkit for custom multiple sequence alignment workflows. It can be used to incorporate sequence annotations, such as secondary structure or (DNA) motifs, into the alignment scoring, as well as to customize many other aspects of a progressive multiple alignment workflow.

AVAILABILITY AND IMPLEMENTATION: PRALINE 2 is implemented in Python and available as open source software on GitHub: https://github.com/ibivu/PRALINE/.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Original languageEnglish
JournalBioinformatics
DOIs
Publication statusE-pub ahead of print - 1 Aug 2019

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Multiple Sequence Alignment
Workflow
Sequence Alignment
Work Flow
Alignment
Boidae
Nucleotide Motifs
Python
Open Source Software
Secondary Structure
Computational Biology
Scoring
Annotation
Bioinformatics
Software
Availability
DNA

Bibliographical note

© The Author(s) 2019. Published by Oxford University Press.

Cite this

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title = "Tailor-made multiple sequence alignments using the PRALINE 2 alignment toolkit",
abstract = "SUMMARY: PRALINE 2 is a toolkit for custom multiple sequence alignment workflows. It can be used to incorporate sequence annotations, such as secondary structure or (DNA) motifs, into the alignment scoring, as well as to customize many other aspects of a progressive multiple alignment workflow.AVAILABILITY AND IMPLEMENTATION: PRALINE 2 is implemented in Python and available as open source software on GitHub: https://github.com/ibivu/PRALINE/.SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.",
author = "Dijkstra, {Maurits J J} and {van der Ploeg}, {Atze J} and Feenstra, {K Anton} and Fokkink, {Wan J} and Sanne Abeln and Jaap Heringa",
note = "{\circledC} The Author(s) 2019. Published by Oxford University Press.",
year = "2019",
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language = "English",
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T1 - Tailor-made multiple sequence alignments using the PRALINE 2 alignment toolkit

AU - Dijkstra, Maurits J J

AU - van der Ploeg, Atze J

AU - Feenstra, K Anton

AU - Fokkink, Wan J

AU - Abeln, Sanne

AU - Heringa, Jaap

N1 - © The Author(s) 2019. Published by Oxford University Press.

PY - 2019/8/1

Y1 - 2019/8/1

N2 - SUMMARY: PRALINE 2 is a toolkit for custom multiple sequence alignment workflows. It can be used to incorporate sequence annotations, such as secondary structure or (DNA) motifs, into the alignment scoring, as well as to customize many other aspects of a progressive multiple alignment workflow.AVAILABILITY AND IMPLEMENTATION: PRALINE 2 is implemented in Python and available as open source software on GitHub: https://github.com/ibivu/PRALINE/.SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

AB - SUMMARY: PRALINE 2 is a toolkit for custom multiple sequence alignment workflows. It can be used to incorporate sequence annotations, such as secondary structure or (DNA) motifs, into the alignment scoring, as well as to customize many other aspects of a progressive multiple alignment workflow.AVAILABILITY AND IMPLEMENTATION: PRALINE 2 is implemented in Python and available as open source software on GitHub: https://github.com/ibivu/PRALINE/.SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

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DO - 10.1093/bioinformatics/btz572

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JF - Bioinformatics

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