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. |
| 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 |