Bioinformatics Flashcards
How to use plasmids?
1-Design: Select a suitable plasmid vector
2- Construction: Introduce desired DNA sequences
3- Verification: Confirm the successful construction of the recombinant plasmid.
4- Transformation: Transfer the recombinant plasmid into the target organism.
5- Expression: Cultivate transformed cells t
Selectable marker (Marker gene)
Gene conferring antibiotic resistance trait
Multiple cloning site (MCS)
Region with multiple restriction enzyme recognition sites for inserting foreign DNA.
Reporter Gene
A reporter gene is a gene whose activity serves as a visible or measurable indicator of the activity of other genes.
PCR
What: Technique to amplify DNA fragments.
Why: Replicate DNA for various analyses.
How: Cyclically heat, cool, and extend DNA using primers and DNA polymerase.
Primer design
What: Designing primers that flank a target DNA region for use in PCR.
Why: To amplify specific DNA sequences for various applications such as DNA sequencing and cloning.
How: Utilizing bioinformatics tools to select primer sequences with appropriate length, melting temperature, and specificity to the target DNA region.
Restriction Enzymes -Sticky/Blunt
What: Enzymes that cut DNA at specific recognition sequences.
Why: Used in genetic engineering to manipulate DNA.
How: Recognize specific DNA sequences and cleave them at specific sites.
Ligation
What: Joining DNA fragments together.
Why: Used in molecular biology to create recombinant DNA molecules.
How: DNA ligase enzyme catalyzes the formation of phosphodiester bonds between DNA fragments.
Types of primers for different purposes.
-Normal PCR. [(18-30 bp)]
-Parenthood type PCR. [(Short <15bp)]
-RE- Primers. [(Adding the RE sequence to the primer’s end)]
-Overlapping primers. [(Complement the other primer back)]
Design primers need some specs
1-Types of primers for different purposes.
2- Thermodynamics.
3- GC content.
4- AT ending
5- Length of the primers.
6- Primers dimers and self dimers
Overlapping PCR
Overlapping PCR involves designing primers with overlapping ends to amplify DNA fragments, which can then be joined together to create a fused DNA sequence.
(PCR Done with fragments that have Tails complement to each other)
Extension PCR
PCR done using special primers with Tail
Purification PCR
PCR to amplify the full constructed fragment
Genomics in bioinformatics
involves using computational tools and techniques to analyze, interpret, and manage large-scale genomic data efficiently.
Genomics is a branch of molecular biology that focuses on the:
Structure,
Function,
Evolution,
Mapping,
And Editing of Genomes
Analyzes entire genome, providing comprehensive genetic information.
Whole Genome Sequencing (WGS)
It makes use of high-throughput techniques, such as as WGS, to sequence DNA fragments rapidly and in parallel.
Next-Generation Sequencing (NGS):
Gene structure [Open reading Frame ORF] CDS:
Represents the portion of a gene that potentially encodes a protein product.
Gene orientation
Refers to the directionality of a gene on a DNA strand, either forward (+) or reverse (-) relative to a reference point.
Gene mining
Involves the identification and extraction of genes or genetic information from genomic data.
Annotation
The process of identifying and labeling genes, regulatory sequences, and other functional elements within a genome.
Comparative Genomics
Analyzes genome similarities/differences to understand evolution, functions, and variations.
Phylogenetics
Reconstructs evolutionary relationships using molecular data to build evolutionary trees.
for Gene location (Locus), use:
NCBI, KEGG, UNIPROT
