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FASTA_​Reader_​Component_​Example_​WF

FASTA Reader Component Example Workflow

FASTA Reader Component Example Workflow

This is an example workflow that demonstrates the FASTA Reader component. Here we read protein and gene sequences of all metabolite metabolizing enzymes on HMDB[1]. The files are included within the workflow but are also available at https://hmdb.ca/downloads. From the views of the components,one can see that the sequence length distribution of proteins is identical to that of the genes.

To visualize the length distribution right click on the component and click on "Interactive View: FASTA Reader". We can then filter for sequences of a certain length and revisit the length distribution using the Histogram node.


[1]: Wishart DS, Feunang YD, Marcu A, Guo AC, Liang K, et al., HMDB 4.0 — The Human Metabolome Database for 2018. Nucleic Acids Res. 2018. Jan 4;46(D1):D608-17. 29140435

This is an example workflow that demonstrates the FASTA Reader component. Here we read protein and gene sequences of all metabolitemetabolizing enzymes on HMDB[1]. The files are included within the workflow but are also available at https://hmdb.ca/downloads. From theviews of the components,one can see that the sequence length distribution of proteins is identical to that of the genes.To visualize the length distribution right click on the component and click on "Interactive View: FASTA Reader". We can then filter for sequencesof a certain length and revisit the length distribution using the Histogram node. [1]: Wishart DS, Feunang YD, Marcu A, Guo AC, Liang K, et al., HMDB 4.0 — The Human Metabolome Database for 2018. Nucleic Acids Res.2018. Jan 4;46(D1):D608-17. 29140435 protein.fastagene.fasta.gzWe can directly read gzipped FASTA filesGene Sequenceswith length 1000 or moreProtein Sequenceswith length 334 or morePlot sequence length distributionPlot sequence length distributionFASTA Reader FASTA Reader Row Filter Row Filter Histogram Histogram This is an example workflow that demonstrates the FASTA Reader component. Here we read protein and gene sequences of all metabolitemetabolizing enzymes on HMDB[1]. The files are included within the workflow but are also available at https://hmdb.ca/downloads. From theviews of the components,one can see that the sequence length distribution of proteins is identical to that of the genes.To visualize the length distribution right click on the component and click on "Interactive View: FASTA Reader". We can then filter for sequencesof a certain length and revisit the length distribution using the Histogram node. [1]: Wishart DS, Feunang YD, Marcu A, Guo AC, Liang K, et al., HMDB 4.0 — The Human Metabolome Database for 2018. Nucleic Acids Res.2018. Jan 4;46(D1):D608-17. 29140435 protein.fastagene.fasta.gzWe can directly read gzipped FASTA filesGene Sequenceswith length 1000 or moreProtein Sequenceswith length 334 or morePlot sequence length distributionPlot sequence length distributionFASTA Reader FASTA Reader Row Filter Row Filter Histogram Histogram

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To use this workflow in KNIME, download it from the below URL and open it in KNIME:

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Created by: Temesgen H. Dadi
Created at: 2020-09-17
On NodePit since: 2020-10-31
Last update: 2025-01-22
Created with KNIME version: v4.2.2

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