Searching in Indices
Introduction
General Syntax
Either the field name (e.g., description) or its abbreviation (des) can be used as the index name. All strings, including the search words, are case-insensitive. For example:
searches for the string "elastase" in the des (description) field of the protein databank, PIR.
Search Strings
To search the keywords field of the EMBL databank for "insulin" you might enter:
To search the description field of the EMBL databank for entries which include "acetylchol*" and "receptor", but remove any entries that contain "muscarinic" you might enter:
To search the authors index field of the SWISS-PROT databank to look for entries containing "sanger,f*" but not "coulson,a*", you might use a query like:
Wildcards
Wildcards are useful if, for example, you wish to search for a group of words (e.g., all words starting with "cell" and ending with "ase") or if it is unclear how a word is spelt in a databank.
SRS uses two types of wildcard:
| * | Matches zero or more characters of any value. |
| ? | Matches one character of any value. |
Any number of wildcards can be placed anywhere in a search word.
Note:Placing a wildcard at the start of a word or string may increase the response time because all words in the index have to be checked against your string.
Regular Expressions
In addition to the use of wildcards, it is also possible to enter regular expressions directly. Regular expressions must appear within forward slashes (/).
Some characters (^$.[]()*+?) have a special meaning these must be prefixed with a backslash (\) to indicate that the specified character is to be matched literally.
Tables and respectively, list typical regular operands and examples of their use.
Note:Searches with regular expressions are sometimes slow since all the words in the index have to be searched.
Searching Using Numerical Ranges
A range can be specified using a single value or by two values separated by a colon (:). The value on the left must be smaller than the value on the right. To exclude a value from the range, put an exclamation mark (!), in front of it. The absence of a number on the left indicates that the search should start at the minimum value in the index. Similarly, an absent value on the right indicates that the search should include values up to the maximum for that index.
| 400 | All sequences with a length of exactly 400. |
| 400:500 | All sequences with lengths between 400 and 500. |
| 400: | All sequences with lengths greater than 400. |
| :500 | All sequences with lengths less than 500. |
| 400:!500 | All sequences with lengths between 400 and 500, excluding 500. |
| : | A range from the minimum value to the maximum value, i.e., all sequences. |
Combining Ranges
Ranges can be combined using logical operators. For instance either:
or
would retrieve the same set of sequences, i.e., all sequences from 300 to 500, excluding 500, and all sequences from 600 to 700, excluding 600.
Searching for Dates
Dates can be used within ranges in the same way as other numbers. For example,
Searching Multiple Databanks
searches for the word, "kinase", in the Description index of the SWISS-PROT, SWISSNEW and SPtrEMBL databanks.
[{swissprot swissnew sptrembl}-des:kinase]
It is often convenient to give a name to a group of databanks so that that name can be used later in the query rather than repeating the list of names. For instance:
creates the group, dbs, which combines the three databanks SWISS-PROT, SWISSNEW and SPtrEMBL, and then uses the group name, dbs, to replace the search name in the second part of the search.
[dbs={swissprot swissnew sptrembl}-des:kinase] &[dbs-org:human]
Note:It is better not to include spaces and other special characters in names as some systems do not handle them properly. Use an underscore, or start new words with a capital letter instead.
