Sequence Flow: interactive web application for visualizing partial order alignments
Tallennettuna:
| Julkaisussa: | BMC Genomics vol. 25 (2024), p. 1 |
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| Päätekijä: | |
| Muut tekijät: | , |
| Julkaistu: |
Springer Nature B.V.
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| Aiheet: | |
| Linkit: | Citation/Abstract Full Text Full Text - PDF |
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| 022 | |a 1471-2164 | ||
| 024 | 7 | |a 10.1186/s12864-024-10886-y |2 doi | |
| 035 | |a 3126413627 | ||
| 045 | 2 | |b d20240101 |b d20241231 | |
| 084 | |a 58495 |2 nlm | ||
| 100 | 1 | |a Zdąbłasz, Krzysztof | |
| 245 | 1 | |a Sequence Flow: interactive web application for visualizing partial order alignments | |
| 260 | |b Springer Nature B.V. |c 2024 | ||
| 513 | |a Journal Article | ||
| 520 | 3 | |a BackgroundMultiple 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.ResultsWe 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.ConclusionsWe 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. | |
| 653 | |a Software | ||
| 653 | |a Exploration | ||
| 653 | |a Alignment | ||
| 653 | |a Source code | ||
| 653 | |a Phylogenetics | ||
| 653 | |a Graphs | ||
| 653 | |a Applications programs | ||
| 653 | |a User satisfaction | ||
| 653 | |a Optimization techniques | ||
| 653 | |a Amino acid sequence | ||
| 653 | |a End users | ||
| 653 | |a Protein structure | ||
| 653 | |a Sequences | ||
| 653 | |a Nucleotide sequence | ||
| 653 | |a Customization | ||
| 653 | |a Structure-function relationships | ||
| 653 | |a Graphical representations | ||
| 653 | |a Phylogeny | ||
| 653 | |a Visualization | ||
| 653 | |a Computer graphics | ||
| 653 | |a Software development | ||
| 653 | |a Environmental | ||
| 700 | 1 | |a Lisiecka, Anna | |
| 700 | 1 | |a Dojer, Norbert | |
| 773 | 0 | |t BMC Genomics |g vol. 25 (2024), p. 1 | |
| 786 | 0 | |d ProQuest |t Health & Medical Collection | |
| 856 | 4 | 1 | |3 Citation/Abstract |u https://www.proquest.com/docview/3126413627/abstract/embedded/7BTGNMKEMPT1V9Z2?source=fedsrch |
| 856 | 4 | 0 | |3 Full Text |u https://www.proquest.com/docview/3126413627/fulltext/embedded/7BTGNMKEMPT1V9Z2?source=fedsrch |
| 856 | 4 | 0 | |3 Full Text - PDF |u https://www.proquest.com/docview/3126413627/fulltextPDF/embedded/7BTGNMKEMPT1V9Z2?source=fedsrch |