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6.1. Searching by text - STRINGSEARCH

Each database entry has one line of text called the "definition". This is an attempt to cover all the salient points, including the PRIMARY accession number, in just 500 letters. The remaining text of the entry includes authors, keywords, secondary accession numbers and more copious descriptions.

6.1.1. Definition search

A search of all the definition lines is much quicker than a full search. This example is a search for two "text patterns": 'Human' and 'Platelet'. When the job has completed, type the output file PLATELET.STRINGS.

$ Stringsearch

STRINGSEARCH through what sequence(s) (* GENEMBL:* *) ?

Do you want to search through:
A) definitions (finds PRIMARY accession numbers)
B) Complete sequence records (finds 2ndry accession nos)

Please choose one (* A *) ?

Search for what text patterns (* Pseudo *) ? Human,platelet

Match patterns by AND or by OR (* AND *) ?

What should I call the output file (* GENEMBL.Strings *) ? platelet.strings

Submit to which batch queue (* MEDIUM *) ? Offpeak

6.1.2. Full text search

$ Stringsearch

STRINGSEARCH through what sequence(s) (* GENEMBL:* *) ? EM_MA:*

Do you want to search through:
A) definitions (finds PRIMARY accession numbers)
B) Complete sequence records (finds 2ndry accession nos)

Please choose one (* A *) ? B

Search for what text patterns (* Pseudo *) ? maniatis,globin,intron

Match patterns by AND or by OR (* AND *) ?

Match how many of the patterns 1-3 (* 3 *) ? 2

What should I call the output file (* EM_MA.Strings *) ? mam.strings

Submit to which batch queue (* LONG *) ?

When more than two patterns are given in an AND search, define the minimum number of obligate matches ie: select 2/3 or 3/4). An 'OR' search finds entries containing any one pattern.

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