I am interested in ESTs. How do you select which ones from GenBank to display in the Genome Browser?
Response: All ESTs in GenBank on the date of the track data freeze for the given organism are used – none are discarded. When two ESTs have identical sequences, both are retained because this can be significant corroboration of a splice site. ESTs are aligned against the genome using the Blat program. When a single EST aligns in multiple places, the alignment having the highest base identity is found. Only alignments that have a base identity level within a selected percentage of the best are kept. Alignments must also have a minimum base identity to be kept. For more information on the selection criteria specific to each organism, consult the description page accompanying the EST track for that organism. The maximum intron length allowed by Blat is 500,000 bases, which may eliminate some ESTs with very long introns that might otherwise align. If an EST aligns non-contiguously (i.e. an intron has been spliced out), it is also a candidate for the Spliced EST track, provided it meets var
