How to find genes? Mining, sequencing, and annotation Flashcards
what is nucleic acid isolation
is the process of extracting DNA or RNA from biological sample such as cells, tissues or microorganisms.
what is gel electrophoresis
is the laboratory technique used to analyze and separate the nucleic acids (RNA and DNA) or protein based on their charge and size.
what is southern blotting
-a technique that is used to detect specific DNA sequence within the mixture of the DNA sequences.
-is the process where DNA segment is transferred from agarose gel to the membrane of host for further analysis such as hybridization
what is DNA Hybridization
is technique of joining two complementary strands of DNA to form double stranded molecule (dsDNA)
what is DNA Sequencing
refer to the method used to determine the specific order of nucleotides(adenine, guanine, cytosine, and thymine) in the DNA strand molecule.
ex: ACCTTGGCAT
what is Polymerase Chain Reaction
is the method that allow for the amplification of specific DAN sequence.
what is DNA Cloning and Restriction Digestion
DNA Cloning: refers to creation of multiple copies of the DNA segment
Restriction Digestion: is the technique used to cut DNA at specific sequence in order to allow manipulation of DNA segment.
what are the key aspects of restriction digestion
- restriction enzyme: are protein that recognize specific short sequence of the DNA and cut DNA or near it. and each restriction enzyme has the unique recognition
what are Genetically encoded molecules
refers to the biological molecule that are synthesized based on the genetic information contain within the organisms.
what is genome mining
is the process of analyzing and exploration of the genomic data to characterize and identify the gene
what does genome mining seek for
is discovering of new genes and pathway involves in biosynthesis of natural product.
what does genome mining used for
to understand the gene responsible for producing those specific metabolite
what is the metabolite
is the compounds that involved in metabolic pathways discovered through genome mining
what is Classical Genome Mining
is a method used to identify biosynthesis gene cluster (BGCs) in genomes
what is biosynthesis gene cluster (BGCs)
are group of genes that work together to produce specific metabolite.
what are different type of genome mining
- classical genome mining
- comparative genome mining
- cultural independent mining: single cell and metagenomes
-resistance base mining
what is Comparative genome mining
this is the method that improve classical genome mining where it uses comparative analysis of multiple genome by enhancing the identification and characterization of their biosynthetic pathways
explain different Comparative genome mining
- correlative based matching: is identification of relationship between gene and their metabolites across different species. for example to identify the presence of GCFs (gene cluster families) in the genome of the strains.
- feature based matching: this methods is based on the specific characteristic of the gene such as biochemical properties.
- co-expression based matching: analyze expression patterns of various condition
how to perform correlative based matching, feature based matching and co-expression based matching respectively
-by calculating correlation coefficient we can establish the link between the BGCs and the metabolites they produce. where the bigger correlation coefficient signifies the strong relationship between BGC and metabolites.
- compare known features of biosynthetic pathways or gene sequence with those from organisms
- by examining co-expression network, we can know the co-expression gene and their potential interaction. if the gene exhibit similar expression pattern they are likely to involves in the same metabolic pathways.
what is the use of correlation based matching, feature based matching and co-expression based matching respectively
- CBM: used to identify the function of unknown gene based on their correlation with known metabolite
- FBM: identify uncharacterized gene by linking them to known features of similar pathway
-COBM: identify the function of uncharacterized gene
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what is Culture independent mining
refers to the extraction and analysis of environment DNA to discover natural product and biosynthetic gene cluster that can not be cultured in the lab
what is environmental DNA
is mining the DNA directly from the environment sample
differentiate between genomics, transcriptomics, proteomics, and metabolomics
genomics: here you sequence all gene
transcriptomics: here you sequence all RNA/DNA
proteomics: here you you identify every protein in that strains
metabolomics: here you you identify all metabolisms
what is dereplication or prioritization
- dereplication: is screening and identifying known compound in the sample
- prioritization: refers to selecting of specific compound or GBCs according to predefine criteria
differentiate between heterogenous expression, synthetic biology and chemical screening
heterogenous expression: refers to inserting/ introducting gene of one organism into different host organism to produce desired molecule/protein.
synthetic biology: is the combination of biology and engineering to design and construct biology parts.
chemical screening: is the identification of active compounds by testing different chemical against specific target
DNA sequencing
tells us the genetic information present in the particular DNA
what is the Sanger sequencing/ chain-termination sequencing
is the methods that are used to determine the nucleotide sequence of DNA
what are DNA sequencing technique
- sanger DNA sequencing
- shotgun DNA sequencing strategies
3, new generation sequencing - 3 and 4 sequencing
- sequencing by binding
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