SMARCA5

---

Description

Main goal of this application is based on making an alignment of any sequence (like protein, DNA, RNA ect.) to its subsequence (f.e. peptides). Visualisation of this proces is done by parsing an output into HTML and CSS, so you only need browser to see the result in clear way. In addition, SMARCA5 calculates basic statistic of any subsequence which are displayed on mouse hoover. If you have result from more than one experiment you will be able to switch a view between them (you can even divide it on group and samples).

---

Requirements

File formats

Sequence

The sequence data should be .fasta or simple .txt file format.

Subsequence

The best way to represent subsequence data is .csv or .xlsx file format. Column name are specific and must look like this:

Sequence	Experiment	Protein
MMAVA	Exp1	SMARCA5
KKKMV	Exp2	SMARCA5; SMARCA5.1
........	..........	..................

In Sequence column you should put your subsequence that you obtain from experiment

In Experiment column you should put your experiment label in given format (like below):

<groupName>_<treatmentType><sampleNumber>

In Protein column you should put information about form which protein this subsequence come (it can be found in databases like UnitProt). If subsequence is not unique (appears in more than one protein) put ;(semicolon) delimiter between them.

---

Display options

SMARCA5 provides two style format to change:

1. Line length
   • it allows you to display more aminoacids in one line
2. Interline (given in pixels)
   • it allows you to increase or decrease space between lines

DEMO

1. Load .fasta and .csv file.
2. Adjust line lenght and interline options.

3. Click Anlayze button.
4. After this new browser tab should pop up.

5. You can display subseqence details by mouse hover

6. Menu (on right side) allows you to switch a view between different experiments

(Photo)

Installation

Clone repo

1. Clone git repo

git clone https://github.com/KubaOfca/SMARCA5.git
git cd SMARCA5

2. Install Poetry (python packaging and dependency management)
3. Use Poetry to create and activate the environment by typing:

poetry shell

4. Install SMARCA5 dependencies by typing:

poetry install

Download .exe version