NCBI databases and Intro to Seq Alignments Flashcards
What is a genomic clone?
- A genomic clone is a piece of genomic DNA inserted into a vector.
- Large genomic clones require special vectors such as YACs (yeast artificial chromosomes) or BACs (bacterial artificial chromosomes).
What can be determined from interest from the sequence of an actual “genomic clone”.
The sequence upstream/downstream from the promoter of our gene of interest from the sequence of an actual “genomic clone”.
Why is Physical Genomic DNA Is Useful?
If you want to express a gene in a transgenic animal in all of the right tissues you will need a large amount of upstream/downstream DNA so that you have the right enhancers.
When Is Knowing the Sequence Enough?
- We can obtain the sequence alone (not the physical DNA itself) from the consensus sequence derived from whole genome sequencing.
- Large stretches of continuous sequences are often called “contigs” for contiguous sequences or “assembly” for assembled sequences.
- For example, knowing the sequence would be sufficient for identifying any consensus binding sequences for transcription factors or identifying related genes or designing PCR primers.
The Genomic Context for PAX6
PAX 6 is on the “minus strand” close to other genes
How is variation as Important as Consensus?
With the sequencing of the human genome, and the drop in the cost of sequencing, we are interested in not just the most common “consensus” sequences but in genetic variation.
SNPs: How do Polymorphisms Underlie Genetic Variation?
As a rule of thumb a genetic variant that occurs in >1% of the population is a polymorphism (mutations are much less frequent)
What are SNPs (Single Nucleotide Polymorphisms)?
a single nucleotide is exchanged for a different nucleotide in at least 1% of the population.
Why Map SNPs?
SNPs are used in associating diseases with genes. Identifying relevant SNPS may allow personalized medicine—the right drug at the right dosage for the individual.
TRUE or FALSE: SNPs are the only source of variation that contribute to disease; copy number variation is not important.
SNPs are not the only source of variation that contribute to disease; copy number variation may be more important.
Give an Example of a SNP
Double stranded DNA of a single allele:
99% of the population: CaTG
GtAC
1% of the population: CgTG
GcAC
Reminder: We all have two alleles for each gene (one
paternal and one maternal). The two alleles may or
may not display the same sequence—If you have a SNP,
you can be homozygous or heterozygous for the SNP).
Most SNPs Are in Non-Coding Regions
Over 1.4 million (SNPs) were identified in the HumanGenome Project, of which 60,000 were in coding regions (Currently about 660 million RefSNPs for humans on dbSNP)
SNPs are most likely to make a difference if they are in a coding region or in a gene regulatory region such as a promoter or a transcription-factor binding site.
Reminder: Not all SNPs in the coding region will result in changes in the amino acid sequence.
To get an optimal alignment, we want to look locally and allow gaps.
Why Look for Local Homology?
Gaps make sense because of the domain structure of proteins.