CIAlign: A highly customisable command line tool to clean, interpret and visualise multiple sequence alignments.
View / Open Files
Publication Date
2022Journal Title
PeerJ
ISSN
2167-8359
Publisher
PeerJ
Volume
10
Language
eng
Type
Article
This Version
VoR
Metadata
Show full item recordCitation
Tumescheit, C., Firth, A. E., & Brown, K. (2022). CIAlign: A highly customisable command line tool to clean, interpret and visualise multiple sequence alignments.. PeerJ, 10 https://doi.org/10.7717/peerj.12983
Abstract
BACKGROUND: Throughout biology, multiple sequence alignments (MSAs) form the basis of much investigation into biological features and relationships. These alignments are at the heart of many bioinformatics analyses. However, sequences in MSAs are often incomplete or very divergent, which can lead to poor alignment and large gaps. This slows down computation and can impact conclusions without being biologically relevant. Cleaning the alignment by removing common issues such as gaps, divergent sequences, large insertions and deletions and poorly aligned sequence ends can substantially improve analyses. Manual editing of MSAs is very widespread but is time-consuming and difficult to reproduce. RESULTS: We present a comprehensive, user-friendly MSA trimming tool with multiple visualisation options. Our highly customisable command line tool aims to give intervention power to the user by offering various options, and outputs graphical representations of the alignment before and after processing to give the user a clear overview of what has been removed. The main functionalities of the tool include removing regions of low coverage due to insertions, removing gaps, cropping poorly aligned sequence ends and removing sequences that are too divergent or too short. The thresholds for each function can be specified by the user and parameters can be adjusted to each individual MSA. CIAlign is designed with an emphasis on solving specific and common alignment problems and on providing transparency to the user. CONCLUSION: CIAlign effectively removes problematic regions and sequences from MSAs and provides novel visualisation options. This tool can be used to fine-tune alignments for further analysis and processing. The tool is aimed at anyone who wishes to automatically clean up parts of an MSA and those requiring a new, accessible way of visualising large MSAs.
Keywords
Comparative genomics, Multiple sequence alignment, phylogenetics, Transcriptomics, Alignment Quality, Python Tool
Sponsorship
Wellcome Trust (106207/Z/14/Z)
European Research Council (646891)
Identifiers
35310163, PMC8932311
External DOI: https://doi.org/10.7717/peerj.12983
This record's URL: https://www.repository.cam.ac.uk/handle/1810/336297
Statistics
Total file downloads (since January 2020). For more information on metrics see the
IRUS guide.
Recommended or similar items
The current recommendation prototype on the Apollo Repository will be turned off on 03 February 2023. Although the pilot has been fruitful for both parties, the service provider IKVA is focusing on horizon scanning products and so the recommender service can no longer be supported. We recognise the importance of recommender services in supporting research discovery and are evaluating offerings from other service providers. If you would like to offer feedback on this decision please contact us on: support@repository.cam.ac.uk