Appendix¶
Query operators¶
Various query forms have operators for use with field values. Available operators are:
=
Exact match (case-insensitive).
contains
Match to a partial string (case-insensitive), e.g. searching for clonal complex ‘contains’ st-11 would return all STs belonging to the ST-11 complex.
starts with
Match to values that start with the search term (case-insensitive).
ends with
Match to values that end with the search term (case-sensitive).
>
Greater than the search term.
>=
Greater than or equal the search term.
<
Less than the search term.
<=
Less than or equal the search term.
NOT
Match to values that do not equal the search term (case-insensitive).
NOT contain
Match to values that do not contain the search term (case-insensitive).
Sequence tag flags¶
Sequences tagged in the sequence bin can have features indicated by specific flags. The presence of these flags can be queried. These are a superset of flags available for allele sequences. Available flags are:
alternative start codon
A start codon other than ATG, GTG, or TTG is used. This can be the case with some yeasts.
ambiguous read
Genome sequence contains ambiguous nucleotides in coding sequence.
apparent misassembly
Sequence has a region of very high identity to existing allele in one region but looks completely different in another.
atypical
Catch-all term for a sequence that is unusual compared to other alleles of locus.
contains IS element
Coding sequence is interrupted by insertion sequence.
downstream fusion
No stop codon present resulting in translation continuing.
frameshift
Frameshift in sequence relative to other alleles, not resulting in internal stop codon.
indel
Insertion/deletion in sequence that is uncommon compared to other alleles.
internal stop codon
Frameshift in sequence relative to other alleles, resulting in internal stop codon.
no start codon
No apparent start codon in immediate vicinity of usual start.
no stop codon
No stop codon in immediate vicinity of usual stop.
phase variable: off
Coding sequence has a homopolymeric run with a frameshift resulting in a stop codon preventing complete translation.
truncated
Coding sequence is unusually short resulting in a truncated protein (not the same as running off the end of a contig).
upstream fusion
No apparent start codon in immediate vicinity of usual start, likely due to a gene fusion (sequence is transcribed together with upstream coding sequence).
Allele sequence flags¶
Sequences can be flagged with specific attributes - these are searchable when doing a sequence attribute query. These are a subset of flags available for tagged sequences. These are mainly for use with whole genome MLST type data. Multiple flags can be selected by Ctrl-clicking the list. Available flags are:
alternative start codon
A start codon other than ATG, GTG, or TTG is used. This can be the case with some yeasts.
atypical
Catch-all term for a sequence that is unusual compared to other alleles of locus.
contains IS element
Coding sequence is interrupted by insertion sequence.
downstream fusion
No stop codon present resulting in translation continuing.
frameshift
Frameshift in sequence relative to other alleles, not resulting in internal stop codon.
indel
Insertion/deletion in sequence that is uncommon compared to other alleles.
internal stop codon
Frameshift in sequence relative to other alleles, resulting in internal stop codon.
no start codon
No apparent start codon in immediate vicinity of usual start.
no stop codon
No stop codon in immediate vicinity of usual stop.
phase variable: off
Coding sequence has a homopolymeric run with a frameshift resulting in a stop codon preventing complete translation.
truncated
Coding sequence is unusually short resulting in a truncated protein (not the same as running off the end of a contig).
upstream fusion
No apparent start codon in immediate vicinity of usual start, likely due to a gene fusion (sequence is transcribed together with upstream coding sequence).