# How did you annotate your new viral genome without it ? VAZyMolO-2

Vincent Wilde, Bruno Canard, Francois Ferron

► To cite this version:

Vincent Wilde, Bruno Canard, Francois Ferron. How did you annotate your new viral genome without it ? VAZyMolO-2. ViBioM2024, May 2024, Luven, Belgium. hal-04616074

HAL Id: hal-04616074

https://hal.science/hal-04616074

Submitted on 18 Jun 2024

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# How did you annotate your new viral genome without it ?

<figure><img src="image_1.png" /></figure>

AFMB

ARCHITECTURE ET FONCTION
DES MACROMOLÉCULES
BIOLOGIQUES

VAZyMoIO-2

Vincent WILDE¹,², Bruno CANARD¹,², François FERRON¹,²

1. Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, PolytechCase 925, 13009 Marseille, France,

2. European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany

<figure><img src="image_2.png" /></figure>

Aix*Marseille

université

Initiative d'excellence

<figure><img src="image_3.png" /></figure>

Contact me

## Abstract

* Sequencing and Metagenomics lead to mass production of bioinformatic data feeding the virus-vers.

* Need of knowledge-collection that can assimilate and interpret this data.

* Revival and enhancement of VAZyMoIO (2003-2011) (F.Ferron et al., 2005).

* Harnessing the intricate interplay between protein structure and biological function.

* Providing a dynamic and effective solution for annotating new viral genome.

<figure><img src="image_4.png" /></figure>

## Objectives

→ **Curated database**

→ starting point previous VAZyMoIO and **leader** of other families.

→ annotating protein into **modules**.

→ merging **Phylogeny** and **Functional Annotation**.

→ **Web-service**

→ **Search**

user through a protein **sequence** or **keywords** (GO / EC).

→ detecting the **closest well-known virus orthologue**.

→ transferring the orthologue annotation on the query's sequence.

(A.Shannon et al., 2020)

## Methods

### Routine analytic pipeline

<figure><img src="image_5.png" /></figure>

**Motif Search**

Gathered from literature or
Structure Analysis

Example: Motif A → "T-G-D-N"

<figure><img src="image_6.png" /></figure>

Pattern search (regex)

<figure><img src="image_7.png" /></figure>

**Sequence Alignment**

Using pair-wise alignment
"hit and run"

<figure><img src="image_8.png" /></figure>

Clustering with MMseqs2

<figure><img src="image_9.png" /></figure>

**Profile Alignment**

Depending on two previous output
Against the profile of 'each' domain

<figure><img src="image_10.png" /></figure>

Aligning with Muscle

### Specificity

### Sensitivity

### Internal analytic pipeline

<figure><img src="image_11.png" /></figure>

**Structure Analysis**

Internal usage to characterize :

→ structure determination

→ association with a biological function

<figure><img src="image_12.png" /></figure>

Domain validation

## Result -> Processing of **pp1ab** Severe acute respiratory syndrome coronavirus (SARS-CoV-2 - 2697049)

<figure><img src="image_13.png" /></figure>

## Phylogeny

<figure><img src="image_14.png" /></figure>

... and beyond ...

<figure><img src="image_15.png" /></figure>

## Conclusion and Perspectives

→ Project still in development

→ Focusing on **Coronaviruses** towards all **Nidovirales** by :

→ **updating** previous project database VAZyMoIO.

→ following **current** team research :

**replicase of emergent viruses.**

→ Tracing usage to prioritize the processing effort.

→ When enough data is collected, usage of AI assistance.

## Acknowledgements

<figure><img src="image_16.png" /></figure>

C A R E

CORONA ACCELERATED R&D IN EUROPE

<figure><img src="image_17.png" /></figure>

<figure><img src="image_18.png" /></figure>
<figure><img src="image_1.png" /></figure>

AFMB

ARCHITECTURE ET FONCTION
DES MACROMOLÉCULES
BIOLOGIQUES

# How did you annotate your new viral genome without it ?

## VAZyMoIO-2

Vincent WILDE¹,², Bruno CANARD¹,², François FERRON¹,²

1. Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, PolytechCase 925, 13009 Marseille, France,

2. European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany

<figure><img src="image_2.png" /></figure>

Aix*Marseille

université

Initiative d'excellence

Contact me

<figure><img src="image_3.png" /></figure>

## Abstract

* Sequencing and Metagenomics lead to mass production of bioinformatic data feeding the virus-vers.

* Need of knowledge-collection that can assimilate and interpret this data.

* Revival and enhancement of VAZyMoIO (2003-2011) (F.Ferron et al., 2005).

* Harnessing the intricate interplay between protein structure and biological function.

* Providing a dynamic and effective solution for annotating new viral genome.

<figure><img src="image_4.png" /></figure>

## Objectives

→ **Curated database**

→ starting point previous VAZyMoIO and **leader** of other families.

→ annotating protein into **modules**.

→ merging **Phylogeny** and **Functional Annotation**.

→ **Web-service**

→ **Search**

user through a protein **sequence** or **keywords** (GO / EC).

→ detecting the **closest well-known virus orthologue**.

→ transferring the orthologue annotation on the query's sequence.

(A.Shannon et al., 2020)

## Methods

### Routine analytic pipeline

<figure><img src="image_5.png" /></figure>

**Motif Search**

Gathered from literature or
Structure Analysis

Example: Motif A → "T-G-D-N"

<figure><img src="image_6.png" /></figure>

Pattern search (regex)

<figure><img src="image_7.png" /></figure>

**Sequence Alignment**

Using pair-wise alignment
"hit and run"

<figure><img src="image_8.png" /></figure>

Clustering with MMseqs2

<figure><img src="image_9.png" /></figure>

**Profile Alignment**

Depending on two previous output
Against the profile of 'each' domain

<figure><img src="image_10.png" /></figure>

Aligning with Muscle

### Specificity

### Sensitivity

### Internal analytic pipeline

<figure><img src="image_11.png" /></figure>

**Structure Analysis**

Internal usage to characterize :

→ structure determination

→ association with a biological function

<figure><img src="image_12.png" /></figure>

Domain validation

## Result -> Processing of **pp1ab** Severe acute respiratory syndrome coronavirus (SARS-CoV-2 - 2697049)

<figure><img src="image_13.png" /></figure>

## Phylogeny

<figure><img src="image_14.png" /></figure>

... and beyond ...

Tree scale: 10

<figure><img src="image_15.png" /></figure>

## Conclusion and Perspectives

→ Project still in development

→ Focusing on **Coronaviruses** towards all **Nidovirales** by :

→ **updating** previous project database VAZyMoIO.

→ following **current** team research :

**replicase of emergent viruses.**

→ Tracing usage to prioritize the processing effort.

→ When enough data is collected, usage of AI assistance.

## Acknowledgements

<figure><img src="image_16.png" /></figure>

CARE

CORONA ACCELERATED R&D IN EUROPE

<figure><img src="image_17.png" /></figure>

<figure><img src="image_18.png" /></figure>