The values a rvd column takes on non-repeat parts.
Details
AnnoTALE reports as N-terminus whatever the ORF encodes upstream of the
first repeat, and as C-terminus whatever it encodes downstream of the last
one. tell_tales searches each of these
segments with the TALE N- or C-terminal protein profile (hmmsearch).
"NTERM" and "CTERM" mark a canonical TALE terminal domain,
one that can be expected to do its usual job: the match has an E-value of
at most terminus_max_evalue, covers at least
terminus_min_cover of the profile (0.9 by default) and reaches the
end of the profile that adjoins the repeats. "XXXXX" marks any
other segment. An array for which AnnoTALE reported no segment on one side
has no terminus part at the protein level on that side.
A terminus can fail to be canonical in several ways, which
array_report.tsv tells apart (its *_aa_* and
*_dna_* columns, see tell_tales): the segment may
be unrelated sequence where the ORF starts or ends inside a frameshifted
region, its repeat-side part may be in another reading frame, or the
terminus may have lost a large part of its domain. The truncTALEs
of Xanthomonas oryzae have lost the activation domain, and their
C-termini are coded "XXXXX". A smaller internal deletion, such as
the one in the N-terminus of TalC, a major TALE of African
X. oryzae pv. oryzae, leaves a terminus canonical.
These share the rvd column with real RVDs, so code that distinguishes
repeats from termini by value should use this function rather than spelling
the codes out.
See also
Other tales objects:
[.tales(),
as_tales(),
format.tales(),
format.tales_msa(),
is_tales(),
new_tales(),
print.tales(),
print.tales_msa(),
summary.tales(),
summary.tales_msa(),
tales(),
tales_anomalies(),
tales_assert_complete(),
tales_bind(),
tales_names(),
tales_namespace(),
tales_requirements(),
validate_tales()