coxdocs/addsequencefeatures.qmd at main · cox-labs/coxdocs · GitHub

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---
title: "Add sequence features"
author: "Cox Lab"
format:
  html:
    toc: true
    toc-depth: 4
    toc-expand: false
    number-sections: true
    number-depth: 4
editor: source
date: today
bibliography: references.bib
---

# General

-   **Type:** - Matrix Processing
-   **Heading:** - Modifications
-   **Source code:** [AddSequenceFeatures.cs](https://github.com/JurgenCox/perseus-plugins/blob/master/PerseusPluginLib/Mods/AddSequenceFeatures.cs)

# Brief description

Site-specific sequence features are added, which were extracted from UniProt.

```{=html}
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The recommended sections are these, but they may be changed on a case by case basis.
===== Detailed description =====
===== Parameters =====
===== Theoretical background =====
===== Examples =====
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```
# Parameters

## Proteins

Selected text column containing the Uniprot IDs (default: first text column of the matrix).

## Positions within proteins

Selected text column containing the positions within the proteins to add site-specific features (default: first text column of the matrix). The column is generated by MaxQuant and is called "Positions".

## Add status column

If checked additional information of Uniprot about the protein sites is added (default: unchecked).

# Parameter window

![](images/modifications-add_sequence_features-edited.png)