This page contains some introduction to the basic queries of the system, and references to the online documentation.

Remember that the query system uses cookies. If results appear 'strange', please clear the 'old' queries by disconnect, then connect again.

connect Return the session_id string to be used in other methods. Do not set username and password to login anonymously.
disconnect Terminate the current session.
seq_list Summary information about all sequence databases.
mot_list Summary information about all motif databases.
cla_list Summary information about all classification databases.
hit_list Summary information about all computed hit lists (sequence vs motif)
hat_list Summary information about all 'hat' lists (sequence vs classification)
hot_list Summary information about all 'hot' lists (motif vs classification)
seq_info Miscellaneous information about sequence databases.
mot_info Miscellaneous information about motif databases.
cla_info Miscellaneous information about classification databases.
seq_hk HitKeeper information about sequence databases.
mot_hk HitKeeper information about motif databases.
cla_hk HitKeeper information about classification databases.
hit_info Miscellaneous information about hit lists (sequence vs motif).
hat_info Miscellaneous information about 'hat' lists (sequence vs classification).
hot_info Miscellaneous information about 'hat' lists (motif vs classification).
seq_parse_name Internal routine not (yet) really useful.
mot_parse_name Internal routine no (yet) really useful
cla_parse_name Internal routine not (yet) really useful.
seq_query For querying the sequences. Refer to HELP(seq_query) for details.
mot_query For querying the motifs. Refer to HELP(mom_query) for details.
cla_query For querying the classifications. Refer to HELP(cla_query) for details.
hit_query For querying the hit lists (sequence vs motif). Refer to HELP(hit_query) for details.
hat_query For querying the 'hat' lists (sequence vs classification). Refer to HELP(hat_query) for details.
hot_query For querying the 'hot' lists (motif vs classification). Refer to HELP(hot_query) for details.
mom_query Advanced query of the list of hits. Refer to HELP(mom_query) for details.
seq_fetch_name Return the non-redundant list of sequence names.
mot_fetch_name Return the non-redundant list of motif names.
cla_fetch_name Return the non-redundant list of classification names.
seq_fetch_desc Return the descriptive text attached to every sequence. This text can be search for using the desc_text constraint of the seq_query() method.
mot_fetch_desc Return the descriptive text attached to every motif. This text can be search for using the desc_text constraint of the mot_query() method.
cla_fetch_desc Return the descriptive text attached to every classification. This text can be search for using the desc_text constraint of the cla_query() method..
seq_fetch_entry Return the non-redundant list of entry text.
mot_fetch_entry Return the non-redundant list of entry text.
cla_fetch_entry Return the non-redundant list of entry text.
seq_fetch_prop Return the non-redundant list of synonyms and property.
mot_fetch_prop Return the non-redundant list of synonyms and property.
cla_fetch_prop Return the non-redundant list of synonyms and property.
seq_fetch_fasta Return the entry in FASTA format.
mot_fetch_fasta Return the entry in FASTA format.
seq_fetch_nr Return the entry in FASTA format (non redundant).
mot_fetch_nr Return the entry in FASTA format (non redundant).
seq_dump_name Return the non-redundant list of sequence names.
mot_dump_name Return the non-redundant list of motif names.
cla_dump_name Return the non-redundant list of classification names.
seq_dump_desc Return the descriptive text attached to every sequence. This text can be search for using the desc_text constraint of the seq_query() method.
mot_dump_desc Return the descriptive text attached to every motif. This text can be search for using the desc_text constraint of the mot_query() method.
cla_dump_desc Return the descriptive text attached to every classification. This text can be search for using the desc_text constraint of the cla_query() method..
seq_dump_entry Return the non-redundant list of entry text.
mot_dump_entry Return the non-redundant list of entry text.
cla_dump_entry Return the non-redundant list of entry text.
seq_dump_prop Return the non-redundant list of synonyms and property.
mot_dump_prop Return the non-redundant list of synonyms and property.
cla_dump_prop Return the non-redundant list of synonyms and property.
seq_dump_fasta Return the entry in FASTA format.
mot_dump_fasta Return the entry in FASTA format.
seq_dump_nr Return the entry in FASTA format (non redundant).
mot_dump_nr Return the entry in FASTA format (non redundant).
hit_fetch_simple Retrieval of hit lists (sequence vs motif).
hat_fetch_simple Retrieval of 'hat' lists (sequence vs classification).
hot_fetch_simple Retrieval of 'hot' lists (motif vs classification).
query_list Return summary information about the query stack
query_info Return the details about the SQL statements: debugging!
query_stat Provides number(s) of rows for the different supported context(s)
query_reset Reset the query stack
default_list Return a few default settings
default_set Alter a few default settings
sticker Prepare a comment to be attached to the next query