Genome annotation Flashcards
Two diff types of genome annotiaton?
Structural and functional
Structural genome annotation?
General idea about what each sequence might be–> has a funciton/doesnt
Functional genome annotation?
More specific idea of what each sequence it–> mRNA (coding), rRNA (noncoding)
What do a lot of genes start with?
ATG–> Methionine
Stop codons?
TAA, TAG, TGA
How can algorithm be designed to search for coding genes?
Look for start and stop codons in appropriate distances
What must be the same ab a start and stop codon of a possible gene?
Must be on the same frame–> within the same multiple of three otherwise they wont be translated together
How many open reading frames are there?
6
Why are there 6 ORFs?
three possible start places in the DNA bc three nucleotides is a codon, *2 bc of the opposite strand of DNA
Why does ORF scanning work better in pro than in eukaryotes?
Smaller genomes, higher gene density, litle gene overlap, introns in eukayotes
What is gene overlap?
Opposite strands that face each other in the nucleotide sequence both coding for genes
Why do introns make it difficult to find possible gene sequences?
They can put the sequence out of frame
What is codon bias?
WHen multiple codons can encode the same AA, diff organisms might have a bias to use some codons to code an AA more than the others that acn code for that AA
Why may codon bias exist?
For organisms to be able to differentiate their DNA from foreign DNA
May affect transcription rate
How can codon bias be used to help estimate where a gene is?
If a sequence has a lot of codons that aren’t really used by that organism to encode the specific AA, it might not be a coding sequence
What is the intron exon boundary?
There is often a GT in between exons and introns
How is homology used to find possible gene sequences?
If a sequence looks similar to a known sequence that is known to code for a gene then that sequence probably codes for a similar gene
Issue with using homology?
If the gene you have found is new/unknown, there wont be homology for it
What are orthologous genes?
present in different species, similar through inheritance from common ancestor
What are paralogous genes?
similar genes within the same species forming a gene family. Often the result of duplications, followed by neo functionalization
What is synteny?
When sequence from different species keep genes in the same order across the chromosome
Benefits of synteny for gene annotation?
Can help confirm predicted genes, and determine function by homology
What was observed when looking for coding genes in synteny?
Many sequences were in synteny across organisms, but were not actually coding genes
Drawbacks of using homology and synteny?
Amplification of mistakes in previous genome sequencing
