Why would I want to look for the x and y sequences from a given EST? Won they form a contig that I can find compiled in a table?
Contigs form when the sequences from the 5′ and 3′ end of the EST overlap in the middle. The longer the cDNA insert, the less likely it is to form a contig. Our experience thus far is that about half of the items sequenced from the 5′ and 3′ (x and y) ends form a contig. These contigs vary in length from ~500 – 1200 bases; the average length varies by library but is usually between 900 – 1000 bases. The other half of the x and y sequences on a single cDNA plasmid failed to contig; either one direction failed to yield usable sequence or the insert size is likely to be >1 kb. Tip: Plasmids with long “x” and “y” sequence that fail to contig in the middle are a good EST to request if you want to obtain more sequence information.
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