CODA – Bioinformatics | Institute of Systems Biology

CODA – Bioinformatics

Bioinformatics analysis is provided for users with own data and the scope depends on users’ requirements. Services ranging from sequencing analysis, protein structure prediction, protein-protein interaction, and gene network analysis to the development of biological database from various omics data. There are four major components in CODA-bioinformatics platform involving sequence-based analysis, structural bioinformatics, network analysis and development of biological database.

1.Sequence-based analysis

In this workflow, bibliomic data that involve information curated from scientific literatures and other databases as well as experimental data are collected, stored and analyzed. Physicochemical prediction and profile analysis from the protein sequence are calculated using various tools such as ProtParam, InterProScan, Pfam and SMART. Glycosylation and phosphorylation sites are also predicted using NetNGlyc and NetPhos respectively. Sequence homology search analysis will be also carried out using appropriate blast programs. Selected sequences from blast analysis will be used for multiple sequence alignment to determine the important conserved regions within the group of proteins of interest. Phylogenetic analysis will be then carried out to see the evolutionary relationships between the protein sequences.

**Flow chart of sequence-based analysis.** There are four major steps in sequence-based analysis that starts with data mining and followed with physicochemical prediction and profile analysis, sequence similarity search and multiple sequence alignment as well as phylogenetic analysis.

2. Structural Bioinformatics

The first step in structural bioinformatics is usually sequence-based analysis to investigate and annotate the protein sequence of interest. Next, structural prediction will be done to uncover the secondary structure, transmembrane helices and disulphide bond properties available in the protein sequence using PSIPRED, TMHMM and DISULFIND respectively. 3D structure will be constructed using possible tools such as I-TASSER, Phyre or SWISS-MODEL. The 3D structure protein will be evaluated using several program tools namely PROCHECK, VERIFY3D and ERRAT2.

**Flow chart of structural bioinformatics.** In this workflow, sequence-based analysis is usually done beforehand to understand the properties of the investigated protein sequence. Next, structural properties such as secondary structure, transmembrane helices and disulphide bonds are predicted. 3D structure prediction will be then constructed and evaluated using the above mentioned bioinformatics tools.

3.Network analysis

Bibliomic and experimental data are usually used as query in constructing a protein-protein interaction (PPI) and biological network. There are several biological network databases that are available such as GeneMANIA, ATTED, STRING, KEGG and Reactome. All of this network data can be visualized using Cytoscape as well as other visualization tools such as Vanted and Gephi. The constructed network will be then analysed for gene ontology enrichment and topological analysis using a number of applications in Cytoscape.

**Flow chart of biological network analysis.** This workflow started out with obtaining biological data from curated scientific literatures or experimental data. Biological network will be then constructed and visualized using suitable tools followed with biological network annotation analysis.

4.Development of biological database

Identification of user requirements

The user needs to list all features that is needed in the database product. If the user does not have a design for the database ready, we will start by proposing the new database to use the same framework as our existing databases. Our databases have these features:

Information pages
Search and advance search function
Browse function
Dashboard/statistics page
Auto adjust of page layout depending on screen resolution
Mobile site included along the desktop site
Modern design through the use of themes

Development of database schema and user interface

From supplied user data, we will identify entities and relationships in the data. We accept data in excel as well as csv files. The database schema will reflect the user’s data as well as the user requirements towards the database’s user interface. We will apply database normalization onto the draft schema to generate the final database schema. The database will be built using MySql and the database user interface will be deployed using Laravel PHP Framework and Bootstrap Frontend. The code will be modular thus each feature of the database will have their own code for easier development in the future of needed.

**Flow chart of development of biological database.** The user needs to list all features that is needed in the database product. If the user does not have a design for the database ready, we will start by proposing the new database to use the same framework as our existing databases.

WHAT DO WE OFFER

We offer bioinformatics consultation and services customized to the needs of the project and available data. Guidelines on the estimated pricing as below. We are also open to other bioinformatics analysis requests other than the ones listed. Do contact us for any inquiries.

Overview of services

Data analysis and bioinformatics

– Sequence-based analysis
– Structural bioinformatics
– Network analysis
– Development of biological database

PRICING DETAILS

TYPE OF ANALYSIS	CHARGES
Sequence analysis	RM 200 / 1,000 sequence
Analysis of protein structure	RM 150/protein
Analysis of biological pathways	RM 500/1,000 sequence
Database development	Database scheme – starting from RM 5,000 SQL Database (data in phpMyAdmin) – starting from RM 2,000 (until 10 entity) Database user interface (PHP controller & frontend) – starting from RM 8,000 (until 10 entity) **Database server and maintenance – starting from RM 2,000 (per annum) Database migration** – RM 2,000