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Figure 5 | BMC Bioinformatics

Figure 5

From: Efficient decoding algorithms for generalized hidden Markov model gene finders

Figure 5

The eclipse() algorithm. Eclipsing signals in queue G when a stop codon has been encountered at position p. All parameters are assumed to be passed by reference. pos(s) is the position of the first base of the signal's consensus sequence (e.g., the A in ATG). len(s) is the length of the signal's consensus sequence (e.g., 3 for ATG). The procedure operates by computing the phase ω in which each signal is eclipsed by the stop codon, and then identifies those signals which are now eclipsed in all three phases. Any signal eclipsed in all three phases is then dropped from the queue, since any exon starting at that signal and extending up to the current position in the sequence would have an in-frame stop codon.

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