Monday, December 21, 2015

Bio (5): Genomics information......

From OriC , the replication fork originates
dnaA gene initiates replication
Use an ORF predictor to predict ORFs.
Then BLAST the ORFs with proteins from database t locate the particular ORF
The DnaA box pattern is lost in bacteria
Human chromosome 21 is the smallest, also the Y chromosome
Genes are conserved at their promoters, TATA box, exons, splice junctions 
#Possible types of genetic mutations
Missense mutation (substitution of one amino acid,  non-synonymous mutation (diff amino acid is formed).)
Nonsense mutation (premature stop signal)
Insertion (adding a piece of DNA)
Deletion (removing a few base pairs)
Duplication (a piece of DNA is copied again)
Frameshift mutation (a gene’s reading frame is altered due to indel)
Repeat expansion (increases the number of times that the short DNA sequence is repeated)
16S rRNA genes: used for taxonomic assignment and phylogenetic trees
Its conserved regions enable simple sample identification using PCR
Metagenome can be collected from variety of ecosystems such as animal and human microbiomes, soils, fresh and salt water samples, plant–microbe interaction systems.

Microarray analysis of transcriptomes is being replaced by RNA sequencing
Organism’s environment is correlated with GC content, genome size, horizontal gene transfer (HGT), optimum growth temperature, and the presence or absence of DnaE2.
Humans carry ten times more bacterial cells than human cells 
DDH: DNA-DNA hybridization (gold standard for bacterial species determination.DDH value of 70 % was widely accepted as the cutoff for separating bacterial species.
16S rRNA analysis replaced DDH technique where a 97 % sequence identity was used to define a new species
Genome scale analysis using reference genomes, groups of conserved proteins, or complete genomes or proteomes is now used for phylogenetic profiling
MicroRNAs (miRNAs/miRs) are a class of small, non-coding RNAs . These miRNAs  target mRNAs.
miR-125a-5p, miR-27a, miR-182, miR-193b
A body function which destroys defunct cells in the body to recycle organelles
Phenotypic variations due on and off of genes due to external stimuli
Heatmap based on a ChIP-seq data (to analyze protein interactions with DNA)
Genetic testing and target capture
Genetic testing of diseases: Bacterial inhibition assay, RFLP, Sanger sequencing, NGS, microarrays
The paradigm of genetic testing has changed in an unprecedented manner.
Identifying the causal gene is difficult, for the pathological condition might have been an outcome of pleotropic genes. The candidate gene number is overwhelming.
Exome sequencing: Sequencing only the ORFs
Target enrichment method: Analyzing only the high-priority parts of the genome (targeted capture)

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