NGS data analysis Services:

We provide comprehensive high-throughput data analysis services. Our bioinformatics offerings include standard as well as highly customized data analysis services along with biological interpretation as per the requirement. Our expertise includes but is not limited to the major next generational sequencing (NGS) workflows for DNA, RNA and small RNA, metadata overlay, data mining, biological contextualization, and  pathway analysis. All workflow steps include data type specific alignment and QC, coupled with powerful Genome Browser explorations to enable visual validations.

Innovative Informatica Technologeis provides range of NGS Data Analysis services from different sequencing platform (illumina, 454, Ion-Torrent, PacBio, Nanopores etc) including

 

  • Whole Genome sequence analysis

  • Whole Exome sequence analysis

  • De novo genome and transcriptome assembly 

  • Genome alignment and analysis 

  • Variant calling

  • Visualization of genomics data

  • Chip-Seq Analysis 

  • Methylome-Seq Analysis 

  • Reference Based RNA-Seq Analysis

  • De-novo Based RNA-Seq Analysis 

  • MicroRNA-Seq Analysis 

  • Targeted re-sequencing (Exome-Seq) Analysis 

  • DNA-Seq (Genome variant Detection) Analysis 

  • Mapping, Annotation and Comparative Genomics Analysis (CGA) 

  • 16S / 28S / ITS rRNA Metagenomic Analysis 

  • Metatranscriptome Analysis 

One of our services specialty is co-relating the Genomics with Proteomics towards identifying the impact of  identified SNPs / mutations on protein structure and functional aspects to their impact on drug discovery. Below are couple of our recent publications for reference:

Sample projects:

A comprehensive Insilico analysis on the structural and functional impact of SNPs in the Congenital Heart Defects associated with NKX2-5 Gene - A Molecular Dynamic Simulation Approach:

 

Project Description: Congenital Heart Defects (CHD) is an important cause of childhood morbidity and mortality worldwide, presented as structural defects in the heart and blood vessels during birth. Many SNPs in different genes have been associated with various types of congenital heart defects. NKX 2-5 gene is one among them, which encodes a homeobox-containing transcription factor that plays a crucial role during the initial phases of heart formation and development. Mutations in this gene could cause different types of congenital heart defects, including atrial septal defect (ASD), atrial ventricular block (AVB), tetralogy of fallot and ventricular septal defect. This highlights the importance of studying the impact of different SNPs found within this gene that might cause structural and functional misbehaviour of its encoded protein. In this study, we retrieved SNPs from the dbSNP database, followed by identificationof potentially deleterious non-synonymous Single nucleotide polymorphisms (nsSNPs) and prediction of their effect on proteins by computational screening using SIFT and Polyphen. Furthermore, we have carried out molecular dynamic simulation (MDS) in order to uncover the SNPs that would cause the most structural damage to the protein, and therefore, altering its biological function. The most important SNP that was found using our approach was rs137852685 (R161P), which was predicted to cause the most damage to the protein’s structural features. Mapping nsSNPs in genes such as the NKX 2-5 gene provides valuable information about individuals carrying those polymorphisms, where such variations can be used as diagnostic markers.

 

Citation: Firoz Abdul Samad, Bandar A Suliman, Syed Hussain Basha, Manivasagam T, Musthafa Mohamed Essa : A comprehensive Insilico analysis on the structural and functional impact of SNPs in the Congenital Heart Defects associated with NKX2-5 Gene - A Molecular Dynamic Simulation Approach: PLoS ONE  (2016)11(5): e0153999. doi:10.1371/ journal.pone. 0153999.

Impact of SNP mutations on the structural and functional behavior of CD44 associated with Oral cancer:

 

Project Description: Oral cancer is a most prevalent cancer worldwide. Natural products are promising resource nowadays in research. Hence, Quinine was selected for the present study. CD44, a trans-membrane glycoprotein is a main hyaluronic acid(HA)binding receptor, expressed in cells, exhibits high affinity towards HA, increasing tumorigenesis. Altered CD44 glucosylation site, affects binding. Hence, computational modelling, simulation approach is applied to understand the effect of variants on the overall structure, functionality of the CD44.Present study demonstrates, T27A mutations affecting the protein structural stability hindering the function. Our simulation studies for CD44 in complex with quinine a natural compound, in its wild type and T27A mutant version state elucidated that due to mutation, protein has lost the required conformational space to recognize, bind the Quinine potentially tight,but not with wild state..

 

Citation: M. Krishnaveni and Syed Hussain Basha : Impact of SNP mutations on the structural and functional behavior of CD44 associated with Oral cancer: International Journal of Pharmacy and Biological Sciences  (2018) 8(2): 352-364.

 

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