BIOLOGY 1A03 Study Guide - Expressed Sequence Tag, Functional Genomics, Plasmid

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Published on 20 Apr 2013
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BIO April 2
Expressed sequence tag: EST (often examined from perspective of coding
RNA)
Functional genomics-> assign a function to the entire gene/protein
Microarrays-> use gathered genomic info to carry out a technique that counts
the expression of target gene in 2 RNA sets
Fold coverage-> gather data that comes from repeated sequences (higher
fold coverage is better) to understand any redundancies (multiple codons for
one a.a)
Annotating the sequence is similar to cataloguing the genes (like a curator in
a museum) -> categorize by type and function
Bacterial artificial chromosomes: BAC -> has no essential genes for survival
of organism but contains parts necessary for replication -> not a plasmid
Portions of bp near the beginning or end of the sequences are more like it to
be ambiguous-> reason why fold coverage is encouraged
Craig Venter sped up sequencing by using whole genome shotgun sequencing
In hierarchical shotgun sequencing you are able to do preliminary overlap
using the BACs
If preparing DNA with restriction enzymes do not do a complete digestion
b/c every site will be used and no overlap between fragments will be present
-> partial digestion is ok
During assembly you ideally want 1 chromosome per protein (?)
Need at least 5 fold coverage to solve ambiguities
Open reading frames: ORFs
EST data helps to assign specific sequences to specific locations on the gen
A lot of junk DNA is micro RNA
Having on ORF makes it likely that this sequence is coding for a gene

Document Summary

Expressed sequence tag: est (often examined from perspective of coding. Functional genomics-> assign a function to the entire gene/protein. Microarrays-> use gathered genomic info to carry out a technique that counts the expression of target gene in 2 rna sets. Fold coverage-> gather data that comes from repeated sequences (higher fold coverage is better) to understand any redundancies (multiple codons for one a. a) Annotating the sequence is similar to cataloguing the genes (like a curator in a museum) -> categorize by type and function. Bacterial artificial chromosomes: bac -> has no essential genes for survival of organism but contains parts necessary for replication -> not a plasmid. Portions of bp near the beginning or end of the sequences are more like it to be ambiguous-> reason why fold coverage is encouraged. Craig venter sped up sequencing by using whole genome shotgun sequencing. In hierarchical shotgun sequencing you are able to do preliminary overlap using the bacs.