Treffer: Sequence Flow: interactive web application for visualizing partial order alignments.

Title:
Sequence Flow: interactive web application for visualizing partial order alignments.
Authors:
Zdąbłasz K; Institute of Informatics, University of Warsaw, Banacha 2, Warszawa, 02-097, Poland., Lisiecka A; Institute of Informatics, University of Warsaw, Banacha 2, Warszawa, 02-097, Poland., Dojer N; Institute of Informatics, University of Warsaw, Banacha 2, Warszawa, 02-097, Poland. dojer@mimuw.edu.pl.
Source:
BMC genomics [BMC Genomics] 2024 Oct 16; Vol. 25 (1), pp. 973. Date of Electronic Publication: 2024 Oct 16.
Publication Type:
Journal Article
Language:
English
Journal Info:
Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164 (Electronic) Linking ISSN: 14712164 NLM ISO Abbreviation: BMC Genomics Subsets: MEDLINE
Imprint Name(s):
Original Publication: London : BioMed Central, [2000-
MeSH Terms:
Internet* , Software* , Sequence Alignment*/methods, Computational Biology/methods ; User-Computer Interface ; Computer Graphics
References:
Bioinformatics. 2015 Oct 15;31(20):3350-2. (PMID: 26099265)
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Nucleic Acids Res. 2001 Jan 1;29(1):323-6. (PMID: 11125126)
Bioinformatics. 2002 Mar;18(3):452-64. (PMID: 11934745)
BMC Bioinformatics. 2019 Nov 5;20(1):548. (PMID: 31690272)
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Bioinformatics. 2019 Aug 15;35(16):2853-2855. (PMID: 30596893)
Bioinformatics. 2022 Jun 27;38(13):3319-3326. (PMID: 35552372)
Grant Information:
01/IDUB/2019/04 Polish Ministry of Science and Higher Education; 01/IDUB/2019/04 Polish Ministry of Science and Higher Education; 01/IDUB/2019/04 Polish Ministry of Science and Higher Education
Contributed Indexing:
Keywords: Multiple sequence alignment; Partial order alignment; Sankey diagram; Webserver
Entry Date(s):
Date Created: 20241016 Date Completed: 20241017 Latest Revision: 20241019
Update Code:
20250114
PubMed Central ID:
PMC11483981
DOI:
10.1186/s12864-024-10886-y
PMID:
39415087
Database:
MEDLINE

Weitere Informationen

Background: Multiple sequence alignment (MSA) has proven extremely useful in computational biology, especially in inferring evolutionary relationships via phylogenetic analysis and providing insight into protein structure and function. An alternative to the standard MSA model is partial order alignment (POA), in which aligned sequences are represented as paths in a graph rather than rows in a matrix. While the POA model has proven useful in several applications (e.g. sequencing reads assembly and pangenome structure exploration), we lack efficient visualization tools that could highlight its advantages.
Results: We propose Sequence Flow - a web application designed to address the above problem. Sequence Flow presents the POA as a Sankey diagram, a kind of graph visualisation typically used for graphs representing flowcharts. Sequence Flow enables interactive alignment exploration, including fragment selection, highlighting a selected group of sequences, modification of the position of graph nodes, structure simplification etc. After adjustment, the visualization can be saved as a high-quality graphic file. Thanks to the use of SanKEY.js - a JavaScript library for creating Sankey diagrams, designed specifically to visualize POAs, Sequence Flow provides satisfactory performance even with large alignments.
Conclusions: We provide Sankey diagram-based POA visualization tools for both end users (Sequence Flow) and bioinformatic software developers (SanKEY.js). Sequence Flow webservice is available at https://sequenceflow.mimuw.edu.pl/ . The source code for SanKEY.js is available at https://github.com/Krzysiekzd/SanKEY.js and for Sequence Flow at https://github.com/Krzysiekzd/SequenceFlow .
(© 2024. The Author(s).)