reverse Flashcards
identification of functionally important sections of a sequenced genome. Coding genes, Noncoding parts (e.g. regulatory elements)
Annotation
(higher % of certain tRNAs in the cell)? : Relative Synonymous codon Usage (RSCU): Note the excess of A ending synonymous codons
Translation efficiency
alignment searches, Retrieve sequences in a database similar to a query. Sacrifices in alignment quality (scores) for speed and ability to retrieve as many matches as possible. not good tool to do alignments to compare sequences
BLAST
For each cloned cDNA, sequence a short segment from the 5’ or 3’ end.
ESTs (Expressed Sequenced Tags):
All DNA content/information in a haploid cell.
Genome
The information content of genomes
Bionformatics
An assembly of contiguous stretches of (chromosomal) DNA. (getting the DNA and sequencing, and put together into something that can be read)
Structural genomics
Characterize the role (level of expression, biological function) played by transcripts and proteins. (what does this tell me? ABCD? what’s the launguge, like reading a book)
Functional genomics
Comparing genomes from different organisms (sequence conservation, nucleotide composition bias). ( learn lessons from comparing genomes, conservation? mutations not allowed here over millions of years. What are things that are rapidly changing?)
Comparative genomics
Use random markers, Organize (map) segments of DNA, Choose minimum number of overlapping clones (tiling path), Sequence (use random markers to make map, then sequence minimum number to make whole thing.)
Hierarchical genome shotgun (HGS)
Fragment the entire genome into pieces, Sequence all pieces, Assemble all pieces into contigs that span each chromosome
Whole genome shotgun (WGS)
It is the average number of times a base is sequenced in a genome project
Coverage
is a universal file format used to report sequences. A FASTA file has a description header starting with >. It is followed by the actual sequence
FASTA
is measured by a score that reflects the number of times a base was identified by the automated sequencer and the quality of the chromatogram for each base (i.e. peak height and even spacing)
Quality
is a four coloured graph produced by the sequencer (chromatogram)
Trace
to switch off deliver in a double strand RNA into fly cell so it will think its weird and attack. So make the RNA complementary to the gene of interest. So attacked by dicer so dicer chops up into segments recognized by RISC that makes then single. a complex also binds to it. Now they have complimentary single strands that bind with the gene of interest (mrna) and then this gets chopped off because its now double stranded RNA again. Double stranded RNA (dsRNA) deliver into cell/ organism. dsRNA is cleaved by Dicer. The short dsRNA can inhibit expression of a gene with complementary sequence by the action of RNA-induced silencing complex (RISC). A specific gene can be targeted and shutdown by delivering dsRNA.
RNA interference
steps for immunity: adaption, crRNA biogenetics, interference. 1. genome specific crRNA sequence, 2)genomic specific trcrRNA-crRNA chimera, 3)a sequence motif like PAM. Crisper sends cas9 to cut a specific RNA sequence it saved thus deleting or inserting certain sequences in the dNA (By Non-homologous end joining (NHEJ) Leads to insertion/ deletion)
CRISPER Cluster of Regularly Interspaced Short Palindromic Repeats.
Remove cells from patient with the disease and make them transgenic with the introduction of the wild-type gene. Reintroduce into patient, immuno deficiencies.
Somatic gene therapy
Correction of the disease and transmission of the normal genotype to the progeny –mitochondrial diseases –CRISPR editing? EX: Transfer of spindle chromosomal complex between donor and recipient cells. Tested in humans as a viable approach to avoid transmission of serious mitochondrial diseases. The technique isolates and transplants the chromosomes (nuclear genetic material) from a patient’s unfertilized oocyte into the cytoplasm of another enucleated egg, containing healthy mtDNA. progeny also cured
Germ-line gene therapy
Attacks proliferating cells (many disorders attack cells that rarely divide) Can integrate into patient genome (insertional mutagenesis)
Retrovirus:
Attacks non dividing cells Does not integrate into patient genome (repeated treatments)
Adenovirus:
Run four reactions with addition of different ddNTPs (can not form phosphodiester bond with the next nucleotide to be incorporated termination of elongation). Each reaction contains various truncated labeled DNA fragments that can be separated and identified by gel electrophoresis. Makes a sequence you can read thats complementary to DNA template strand
Sanger method
small circle double stand (dsDNA), ORI, some antibiotic resistance maker, restriction sites
Plasmid
A collection of clones, each containing a different sample of the donor DNA of interest.
DNA library
infect cells with high efficiency. Can take fragments longer than 10Kb. Remember that some eukaryotic genes can be quite long.
Viruses
can carry up to 45Kb long donor DNA. They can replicate as plasmids and can be packaged into phage heads.
Cosmids
(BACs, YACs) can carry longer fragments of DNA (cloning full genomes).
Artificial chromosomes
