Term
| bacterial artificial chromosome (BAC) |
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Definition
| most popular vector for cloning very large DNA inserts (derived from F plasmid) |
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Term
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Definition
allows cloning of a larger sequence (same principle as plasmid)
BAC library = Genomic library |
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Term
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Definition
-how the human genome was first cloned -> cloning a larger region of a chromosome by using a sequence of a nearby landmark as a probe to identify a second set of clones that overlaps the marker clone containing the landmark but extends out from it in one of two direction (end fragments from new sets of clones can be used as probes for identifying third set of overlapping clones from the genomic library)
-want minimal overlap |
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Term
| shotgun sequencing of clone |
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Definition
| take a clone (BAC clone), break up into small fragments, sequence each fragment by shotgun sequencing, overlap sequences to make contigs, overlap contigs for complete sequence (makes big clone) |
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Term
| whole genome shotgun sequencing |
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Definition
| determine the sequence of many segments of genomic DNA that have been generated by breaking the long chromosomes of DNA into many short fragments |
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Term
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Definition
| building up all of the individual reads |
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Term
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Definition
| pairs of sequence reads from opposite ends of the genomic inserts in the same clone (spans gap between two sequence contains) |
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Term
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Definition
| sequences that are contiguous (touching) |
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Term
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Definition
| the identification of all the functional elements of a particular genome |
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Term
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Definition
→ can be transcribed but has not function (a dead gene)
-we have as many dead genes as living genes |
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Term
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Definition
the order of genes within variously sized blocks is the same as their order in the most recent common ancestor of the two species
-mammalian genomes have large segments with the same order of genes (syntenic regions) |
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Term
| Why would part of a gene be missed when sequencing |
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Definition
o Incomplete cDNA clones
o Genes with extremely rare transcripts
o Genes only expressed in a small window of time in a limited tissue during development
o Some genes may not be active (pseudogenes) |
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Term
| How to identify genes in genome after shotgun |
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Definition
-make a ton of cDNA from several different tissues
-search genomic library (from shotgun) with cDNA's |
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