| ... | ... | @@ -14,4 +14,4 @@ The coordinates used for extracting and handling the domain sequences are the en |
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> (“env from” and “env to”) define the envelope of the domain’s location on the target sequence. The envelope is almost always a little wider than what HMMER chooses to show as a reasonably confident alignment. As mentioned earlier, the envelope represents a subsequence that encompasses most of the posterior probability for a given homologous domain, even if precise endpoints are only fuzzily inferrable.
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After domain prediction, a step of filtering is performed where overlapping domains are discarded based on the per-domain score. When comparing pairs of domains within the same CDS, domain filtering will be triggered if the amino acid overlap percentage of any of the domain's sequences (i.e. $`overlap in amino acids / the domain length`$) is higher than `overlap_cutoff` (set by the `--domain_overlap_cutoff` parameter), which is $`0.1`$ by default. |
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After domain prediction, a step of filtering is performed where overlapping domains are discarded based on the per-domain score. When comparing pairs of domains within the same CDS, domain filtering will be triggered if the amino acid overlap percentage of any of the domain's sequences (i.e. overlap in amino acids / domain length) is higher than `overlap_cutoff` (set by the `--domain_overlap_cutoff` parameter), which is $`0.1`$ by default. |
