What are the advantages and disadvantages of a cDNA library compared to a genomic library?

Answer 1

cDNA is made from messenger RNA (mRNA) so contains only the functional coding region. (The introns are spliced out of mRNA.) When the library is constructed not all clones are full length when they are oligo dT primed. The short clones mean several clones are often needed to complete the coding region at the 5' end. If it was a rare mRNA this may be difficult but if it was a common mRNA then one probing usually pulls out enough copies to complete the sequence. (There are also cDNA kits to prime specifically from the 5' as well as the 3' end so you are more assured of getting overlapping clones.) Clones are short and easy to sequence. You do not know where the introns are located so a genomic clone will be needed for that. A cDNA clone is needed to transfect cells for protein production or for cell based assays.

A genomic library will be very unlikely to contain an entire coding region on one clone due to the size of the introns. Several clones would then need to be analyzed for overlap between them. If the cDNA is used the intron donor and acceptor sites can be easily sequence from the known cDNA sequence. If there is no cDNA the entire sequence will have to be done. Introns can be very difficult to sequence if the contain palindromic repeats or long stretches of Alu repeats. Ideally the cDNA copy will be found first to ease & shorten the sequencing needed from the genomic clones. If distant regulation sequences like enhancers are of interest then the genomic clone is necessary.