De-novo genome assembly is typically carried out when a reference genome sequence of a particular organism is not sequenced till date. The process involves putting together overlapping pieces of DNA obtained from sequencing of unknown template DNA (from an organism). It is a computationally intensive process and requires a wide variety of parameters to be adjusted based on the nature of the organism. GIC’s services include draft genome assembly plus detailed genome annotation, which can be visualized in a powerful genome browser environment.

In-silico steps-

• De-novo assembly at different K-mer lengths

• Statistical information of assembled contigs (total number of assembled contigs, size distribution of assembled contigs, average contig size, N50and N90 contig sizes).

• Scaffolding of contigs

• Gap closing and ordering contigs

• Assembly validation

• Genome annotation (structural and functional)

This approach is used to understand the gene expression and regulation in species development and disease. Time series/interval data, data from genetic variants and data from microarray platforms are all supported.

In-silico steps-

• Alignment of transcriptome data to the reference genome

• Transcript assembly

• Detection of novel Genes and isoforms

• Expression analysis

• Differential Expression analysis (if Case-Control experiment/time-series)

• Pathway and GO Analysis

• Gene Fusion Analysis

• Data Visualization

In-silico steps-

• Alignment of transcriptome data to the reference genome

• Transcript assembly

• Multiple filtration process in detection of novel lncRNAs and isoforms

• Expression analysis

• Differential Expression analysis (if Case-Control experiment/time-series)

• Study of potential genes cis and trans targeted by lncRNAs.

• Pathway and GO Analysis of targeted genes.

• Data Visualization.

In-silico steps-

• Alignment of small RNAs transcriptome data to the reference genome

• Screening of 20-25nt sequences

• Detection of novel and reported miRNAs

• Expression analysis (if Case-Control experiment/time-series)

• Target prediction of miRNA

• Pathway and GO Analysis of targeted genes

• Network and Data Visualization

Genome-wide analysis of the DNA methylation patterns by immunoprecipitation of methylated cytosines or based on bisulfite conversion of methylated cytosines to uracil.

In-silico steps-

• Alignment of bisulfite converted reads with respect to the reference genome.

• Detailed mapping of methylcytosine positions.

• Discovery of differentially methylated regions.

• Pathway and GO analysis.

• Data Visualization.

Chromatin immunoprecipitation (ChIP) followed by sequencing is a powerful method to determine the locations of DNA binding sites for a protein (transcription factor) of interest. Determining protein-DNA interactions involved in gene regulation is essential to fully understand biological processes and diseases.

In-silico steps-

• Alignment and fragment length distribution analysis.

• Transcription factor binding site detection / motif discovery.

• Target gene identification.

• Pathway and GO analysis.

We provide all microarray platforms supported Agilent, Affymetrix, and Illumina.

In-silico steps-

• Data quality assessment.

• Data normalization (RMA, MAS5, loess).

• Differential gene expression analysis, including pie charts and clusters, reporting of observations for CGH & CNV arrays.

• Enrichment analysis for chip samples, miRNA detected in easily variable spread sheets.

• Determination of differential gene expression by ANOVA and fold change.

• Clustering Analysis (Hierarchical, K-means, Self Organized Maps, etc.)

• Function and Pathway analysis for statistically significant genes.

• Pathway Enrichment Analysis, Gene Ontology Enrichment Analysis, MetaCore Network Analysis.

In-silico steps-

• Homology modelling.
• Ligand-receptor interaction Docking studies.
• Molecular Dynamics simulation (MD).