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Definition
| analysis of the information content of entire genomes; looking at it and how its organized |
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| provides evolutionary insight and useful as a guide to analyzing gene function |
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Definition
| variety of methods to understand gene function and define networks of interacting genes |
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| why is characterizing whole genomes important |
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Definition
| for a fundamental understanding of the operating principles of living organisms and for the discovery of new genes |
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| whole genome shotgun sequencing |
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Definition
| take the whole genome to sequence |
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| reasons for missing segments of DNA |
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Definition
| repetitive DNA is not clonable in bacteria; DNA polymerase in bacteria can't replicate certain patches of repetitive DNA; you didnt sequence deeply enough |
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| how you put contigs in the right order |
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Definition
| use a plasmid with a huge insert and acquire paired end reads. these end reads will math up with contigs, allowing you to sequence the DNA |
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Definition
| obtain more sequence reads and use PCR to amplify the missing DNA; this is then sequenced |
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Definition
| rarely/never used; took each chromosome separately and sequenced them |
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| Dve terminator sequencing |
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Definition
| complementary strands are made until a ddNTP ends the sequence, this has a dye on it |
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| Capillary electrophoresis |
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Definition
| reach successive length travels through the laser and the color tags are read, allowing you to read the sequence |
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Definition
| identification of all functional elements of the genome |
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| a list of all the proteins made from a genome to determine the list of polypeptides one must deduce all the structural genes in a genome |
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| ORF (open reading freame) detection |
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Definition
| identification of open reading frames; looks for sequences that have the characteristics of genes |
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Term
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Definition
| complementary DNA; is a DNA copy of an NA molecules, most often from mRNA; used to identify genes and what are introns |
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Term
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Definition
| search genome sequences for predicted sequences of various binding sites used for promoters, transcriptions start site, 3' and 5' splice sites and translation initiation sites |
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Definition
| idealized match for a specific protein to DNA recognition event |
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| predictions of mRNA and polypeptide structure from genomic DNA sequence depends on: |
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Definition
| the integration of information from cDNA seuence, binding site predictions polypeptide similarities and codon bias |
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Definition
| the order of genes on a chromosome |
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Definition
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Definition
| genes in different species that evolved from a common ancestral gene, genes retain the same function |
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| genes related by duplication, genes evolve new functions |
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Definition
| the complete set of physical interactions between proteins and DNA segments, between proteins and RNA sequences and between proteins |
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Definition
| used to detect the activity of another protein |
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Definition
| the sequence and expression pattern of all transcrips (where, when, how much) |
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Definition
| interaction with other genes; bait and target |
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| protein under investigation spliced next to the DNA binding domain |
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Definition
| gene for another protein under investigation is spliced to the activation domain |
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Definition
| the most precise means of obtaining mutations in a specific gene and can now be practiced in a variety of model systems |
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Definition
| when double stranded RNA is put inside the cell, it is dstroyed, along with all other RNA matching its sequence |
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Term
| what does RNAi and chemical genomics provide |
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Definition
| ways of experimentally interfering with the function of a specific gene, without changing its DNA sequence |
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