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Remove unnecessary # Introduction section #4484

Merged
merged 1 commit into from
Nov 9, 2023
Merged

Remove unnecessary # Introduction section #4484

merged 1 commit into from
Nov 9, 2023

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hexylena
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@hexylena hexylena commented Nov 3, 2023

Everything above the agenda is already equivalent to an abstract for most tutorials. However many still included a "# Introduction" title that doesn't really bring any utility. So we remove all of those.

This will make it additionally make it easier for us to automatically extract a nice 'abstract' for each tutorial (using the first paragraph.)

In some places I've moved a paragraph up because a comment box was first which also wasn't such a nice UX.

Linting errors are .. very expected.

@@ -24,9 +24,6 @@ contributors:
subtopic: prokaryote
---

# Introduction


In this section we will use a software tool called Prokka to annotate a draft genome sequence. Prokka is a “wrapper”; it collects together several pieces of software (from various authors), and so avoids “re-inventing the wheel”.

Prokka finds and annotates features (both protein coding regions and RNA genes, i.e. tRNA, rRNA) present on on a sequence. Note, Prokka uses a two-step process for the annotation of protein coding regions: first, protein coding regions on the genome are identified using [Prodigal](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2848648/); second, the *function* of the encoded protein is predicted by similarity to proteins in one of many protein or protein domain databases. Prokka is a software tool that can be used to annotate bacterial, archaeal and viral genomes quickly, generating standard output files in GenBank, EMBL and gff formats. More information about Prokka can be found [here](https://github.com/tseemann/prokka).
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🚫 [rdjsonl] <GTN:005> reported by reviewdog 🐶
Please do not use 'here' as your link title, it is bad for accessibility. Instead try restructuring your sentence to have useful descriptive text in the link.

Suggested change
Prokka finds and annotates features (both protein coding regions and RNA genes, i.e. tRNA, rRNA) present on on a sequence. Note, Prokka uses a two-step process for the annotation of protein coding regions: first, protein coding regions on the genome are identified using [Prodigal](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2848648/); second, the *function* of the encoded protein is predicted by similarity to proteins in one of many protein or protein domain databases. Prokka is a software tool that can be used to annotate bacterial, archaeal and viral genomes quickly, generating standard output files in GenBank, EMBL and gff formats. More information about Prokka can be found [here](https://github.com/tseemann/prokka).
Prokka finds and annotates features (both protein coding regions and RNA genes, i.e. tRNA, rRNA) present on on a sequence. Note, Prokka uses a two-step process for the annotation of protein coding regions: first, protein coding regions on the genome are identified using [Prodigal](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2848648/); second, the *function* of the encoded protein is predicted by similarity to proteins in one of many protein or protein domain databases. Prokka is a software tool that can be used to annotate bacterial, archaeal and viral genomes quickly, generating standard output files in GenBank, EMBL and gff formats. More information about Prokka can be found [Something better here](https://github.com/tseemann/prokka).




Several computational methods have been proven very useful in the initial screening and prediction of peptides for various biological properties. These methods have emerged as effective alternatives to the lengthy and expensive traditional experimental approaches. Properties associated with a group of peptide sequences such as overall charge, hydrophobicity profile, or k-mer composition can be utilized to compare peptide sequences and libraries. In this tutorial, we will be discussing how peptide-based properties like charge, hydrophobicity, the composition of amino acids, etc. can be utilized to analyze the biological properties of peptides. Additionally, we will learn how to use different utilities of the Peptide Design and Analysis Under Galaxy (PDAUG) package to calculate various peptide-based descriptors, and use these descriptors and feature spaces to build informative plots.
Several computational methods have been proven very useful in the initial screening and prediction of peptides for various biological properties. These methods have emerged as effective alternatives to the lengthy and expensive traditional experimental approaches. Properties associated with a group of peptide sequences such as overall charge, hydrophobicity profile, or k-mer composition can be utilized to compare peptide sequences and libraries. In this tutorial, we will be discussing how peptide-based properties like charge, hydrophobicity, the composition of amino acids, etc. can be utilized to analyze the biological properties of peptides. Additionally, we will learn how to use different utilities of the Peptide Design and Analysis Under Galaxy (PDAUG) package to calculate various peptide-based descriptors, and use these descriptors and feature spaces to build informative plots.


### Easy access to tools, workflows and data from the docker image
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🚫 [rdjsonl] <GTN:028> reported by reviewdog 🐶
You have skipped a heading level, please correct this.

Listing of Heading Levels
### Easy access to tools, workflows and data from the docker image
## Peptide Data
## Converting tabular data into fasta format
## Analyzing peptide libraries (AMPs and TMPs) based on features and feature space
### Summary Plot for peptide libraries
### Assessing feature space distribution
## Assessing the relation between peptide features by 3D scatter plot
### Calculating Sequence Property-Based Descriptors
### Adding the Class Label in both AMPs and TMPs
### Merging the two tabular data files
### Plotting CTD descriptor data as Scatter plot
# Conclusion
```suggestion ## Easy access to tools, workflows and data from the docker image ```

@shiltemann shiltemann merged commit 58078dc into main Nov 9, 2023
3 of 4 checks passed
@bgruening bgruening deleted the caracara-map branch November 9, 2023 09:36
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