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Bioinformatics

/Bioinformatics
Bioinformatics 2018-02-12T06:08:39+00:00

Bioinformatics is an interdisciplinary field that develops methods and software tools for understanding biological data. As an interdisciplinary field of science, bioinformatics combines Computer Science, Biology, Mathematics, and Engineering to analyze and interpret biological data. Bioinformatics has been used for in-silico analyses of biological queries using mathematical and statistical techniques.

  • Exposure and usage of online DNA & Protein databases
    (NCBI, Ensemble, ENA, UCSC, ExPasy, UniProt, PDB)
  • Primer designing tools
    (Primer3, NetPrimer, OligoCal, Primer Premier)
  • Sanger sequencing and sequence analysis tools
    (Sequencher, BioEdit, CodonCode Aligner, Chromas Lite, DnaSP)
  • Phylogenetics trees construction
    (MEGA and Mathematica software usage)
  • NGS- WGS, RNASeq, Exome Seq, Methyl Seq data analysis, softwares and tools
    (R, Python), (Concept of NGS platforms “NovaSeq, HiSeq, MiSeq)”, library preparation: TruSeq PCR-free, TruSeq nano DNA, Nextera DNA, Nextera DNA XT  library preparation kits, Library quantification and qualification: qPCR or Qubit/bioanalyzer, WGS analysis: concept of Bcl, FASTQ, SAM/Bam files, Aligning softwares/tools: BWA, Bowtie2, Map, Stampy, Novoalign, FastQC and Picard tool, Variant calling softwares/tools: SAMtools mpileup, GATK, Visualization softwares/tools: Integrative genomic viewer, UCSC genome browser, RNASeq Mapping program/tools: TopHat, STAR,   Exome-Seq: same software as with WGS analysis)
  • Genome-wide association study (GWAS) and statistical analysis of genetics and genomics data
    (PLINK data analysis toolset, Haploview software, Test statistics tools through Excel, SPSS and R statistical package)
  • Multiple Sequence Alignment and familiarization to online data analysis tools
    (BLAST, MUSCLE, ClustalW, T Coffee)
  • Real-Time-qPCR
    (Primer/probe designing softwares and online tools “Primer Express”, “DataAssist” )
  • Gene expression data analysis
    (Absolute quantification, Relative quantification: Comparative Ct Method)
  • In-silico analysis of protein
    (Physiochemeical properties, conserved domains, transmembrane structures, posttranslational modifications and structure prediction, In-silico PCR, Protparam, Psipred, Motifscan, Protscale and Scanprosite tools)