INTRODUCTORY BIOINFORMATICS

Module includes:
Introduction to NCBI, UCSC Genome browser.
Primer Designing, BLAST, gene mapping etc.
Databases such as Uniprot, Protein Data Bank, db SNP etc.
Introduction to R for plotting data.
Detailed linux tutorial for executing the NGS tools through command-line.


WHOLE EXOME SEQUENCING
 

Module includes:
NCBI SRA and retrieval of submitted sequences, explanation of various index files and latest draft genome assemblies.
Explanation of file formats including SAM/BAM, VCF, FASTQ. Hands on raw sequences quality analysis on data retrieved from 1000 Genomes Exome Data.
Trimming and improvisation using FastQC, Cutadapt, trimmomatic etc., emphasis on choice of decision, Base Quality Score Recalibration (BQSR).
Alignment quality Control and Coverage Analysis and Plotting Practical usage of tools such as Bowtie and BWA to align the reads with the reference genome.
Identification of SNPs and other variants through GATK tool kit and SAMTOOLS.
Annotation of genes and pathways through KEGG.
Prediction, functional/pathological effect of variants through SIFT algorithm etc.
Visualization through IGV and UCSC browser.
Gene prioritization.

DIFFERENTIAL GENES  EXPRESSION - RNA SEQ

Module includes:
NCBI SRA and retrieval of submitted sequences, explanation of various index files and draft genome assemblies.
Hands on raw sequences quality analysis, trimming and improvisation using FastQC, Cutadapt, trimmomatic etc.
Mapping through TopHat on the reference genome for RNA-Seq reads.
It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie. Assembly of transcripts through Cufflinks tool to estimate their abundances.
Cuffdiff to check for Differential Expression under different conditions.
Application of CummeRbund for generation of plots for interpretation including Density plot of the genes under different conditions, Volcano Plot for differentially expressed genes, scatter plots showing the expression of genes under different conditions, comparative expression of selected genes under different conditions using Bar Plots, identification of genes with similar expression profile to the selected gene, hierarchical clusters and clustered heatmaps etc.

META-GENOMICS NGS

Module includes:

NCBI SRA and retrieval of submitted sequences, explanation of various index files and draft genome assemblies.
Hands on raw sequences quality analysis, trimming and improvisation using FastQC,
Cutadapt, trimmomatic etc.MG-RAST server Workflow, Short Metagenomics (pre-processing, dereplication, screening to remove reads that are near-exact matches to the genomes of model organisms such as fly, mouse, cow and human etc., gene calling.
Filter proteins, Cluster proteins at 90% identity level using uclust, protein identification, annotation mapping, abundance profile, summary report.
16s Metageomics ( RNA detection, clustering and identification, annotation mapping and abundance profiling Plotting of results such as taxonomic classification and relative abundance chart of themicrobial communities
Generation of functional biome tables etc.

MOLECULAR DYNAMICS SIMULATIONS

Module includes:
Comprehensive mastering of protein structure analysis from experimental 3D coordinate data using pyMOL and VMD.
Preparation of the experimental structure for conducting molecular dynamics simulations through structural corrections and modelling.
Setting correct pKa values and pH  of the protein.
Solvation of the corrected protein structure in solvent and addition of physiological salt concentration.
Preparatory and production scale MD simulation.
MD trajectory data analysis eg. RMSD, RMSF, Radius of Gyration, H bonds, free energy maps, secondary structure analysis, intrinsic disorder analysis, PCA, unsupervised clustering, cross correlation maps, networks and betweeness analysis etc.

RESEARCH REPORT WRITING

Module includes:
Effective research article writing, check plagiarism.
Making high resolution scientific images, plots and reference management.
We also guide students on choosingthe right research journals for publication of their work
.