How to find genes? Mining, sequencing, and annotation

Question 1

what is nucleic acid isolation

Answer 1

is the process of extracting DNA or RNA from biological sample such as cells, tissues or microorganisms.

Question 2

what is gel electrophoresis

Answer 2

is the laboratory technique used to analyze and separate the nucleic acids (RNA and DNA) or protein based on their charge and size.

Question 3

what is southern blotting

Answer 3

-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

Question 4

what is DNA Hybridization

Answer 4

is technique of joining two complementary strands of DNA to form double stranded molecule (dsDNA)

Question 5

what is DNA Sequencing

Answer 5

refer to the method used to determine the specific order of nucleotides(adenine, guanine, cytosine, and thymine) in the DNA strand molecule.

ex: ACCTTGGCAT

Question 6

what is Polymerase Chain Reaction

Answer 6

is the method that allow for the amplification of specific DAN sequence.

Question 7

what is DNA Cloning and Restriction Digestion

Answer 7

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.

Question 8

what are the key aspects of restriction digestion

Answer 8

• 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

Question 9

what are Genetically encoded molecules

Answer 9

refers to the biological molecule that are synthesized based on the genetic information contain within the organisms.

Question 10

what is genome mining

Answer 10

is the process of analyzing and exploration of the genomic data to characterize and identify the gene

Question 11

what does genome mining seek for

Answer 11

is discovering of new genes and pathway involves in biosynthesis of natural product.

Question 12

what does genome mining used for

Answer 12

to understand the gene responsible for producing those specific metabolite

Question 13

what is the metabolite

Answer 13

is the compounds that involved in metabolic pathways discovered through genome mining

Question 14

what is Classical Genome Mining

Answer 14

is a method used to identify biosynthesis gene cluster (BGCs) in genomes

Question 15

what is biosynthesis gene cluster (BGCs)

Answer 15

are group of genes that work together to produce specific metabolite.

Question 16

what are different type of genome mining

Answer 16

• classical genome mining
• comparative genome mining
• cultural independent mining: single cell and metagenomes
  -resistance base mining

Question 17

what is Comparative genome mining

Answer 17

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

Question 18

explain different Comparative genome mining

Answer 18

• 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

Question 19

how to perform correlative based matching, feature based matching and co-expression based matching respectively

Answer 19

-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.

Question 20

what is the use of correlation based matching, feature based matching and co-expression based matching respectively

Answer 20

• 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

Question 21

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Answer 21

sudy page 15

Question 23

what is Culture independent mining

Answer 23

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

Question 24

what is environmental DNA

Answer 24

is mining the DNA directly from the environment sample

Question 25

differentiate between genomics, transcriptomics, proteomics, and metabolomics

Answer 25

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

Question 26

what is dereplication or prioritization

Answer 26

• dereplication: is screening and identifying known compound in the sample
• prioritization: refers to selecting of specific compound or GBCs according to predefine criteria

Question 27

differentiate between heterogenous expression, synthetic biology and chemical screening

Answer 27

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

Question 28

DNA sequencing

Answer 28

tells us the genetic information present in the particular DNA

Question 29

what is the Sanger sequencing/ chain-termination sequencing

Answer 29

is the methods that are used to determine the nucleotide sequence of DNA

Question 30

what are DNA sequencing technique

Answer 30

1. sanger DNA sequencing
2. shotgun DNA sequencing strategies
   3, new generation sequencing
3. 3 and 4 sequencing
4. sequencing by binding

Question 31

review by writing here

Answer 31

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