X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Ffeatures%2Funiprotsequencefetcher.html;h=4a64f52ddac49d43eebd68355f179f686af51e14;hb=d5702bf3268c2688e90d645ec635ad5bb5d3a76e;hp=55b4d71c31ad66b542677b8dd98ed564e1247634;hpb=99ab1f82f65f725e02cf9c8ad1cbe3e16f62ad80;p=jalview.git diff --git a/help/html/features/uniprotsequencefetcher.html b/help/html/features/uniprotsequencefetcher.html index 55b4d71..4a64f52 100644 --- a/help/html/features/uniprotsequencefetcher.html +++ b/help/html/features/uniprotsequencefetcher.html @@ -20,142 +20,150 @@ * The Jalview Authors are detailed in the 'AUTHORS' file. -->
-- Jalview provides a specialised interface that allows fast and - efficient discovery and retrieval of data from the Uniprot database. - It allows - interactive querying of Uniprot metadata with free text and structured - queries, so sequences can be located without prior knowledge of - their database accessions, or via manual cross-referencing - from Uniprot or other bioinformatics websites. + To open the UniProt Sequence Fetcher, select UniProt as the database + from any Sequence Fetcher dialog (opened + via "File →Fetch + Sequences").
- To open the UniProt Sequence Fetcher, select UniProt as the database from - any Sequence Fetcher dialog (opened via - "File →Fetch Sequences"). -
-- +
- Searching the Uniprot Database + Searching the UniProt Database
-- To search the Uniprot, begin typing in the text box. The results of your - query are shown in the search results tab, which queries Uniprot after 1.5secs every time - you type in the search text box. You can sort results according to - the displayed columns, and select entries with the mouse or - keyboard. Once you have selected one or more entries, hit the OK - button to retrieve and visualise the sequences in Jalview Alignment interface. +
To search UniProt, simply begin typing in the text box. If the + 'autosearch' check box is enabled, then after a short delay (about + 1.5 seconds), results will be shown in the table below. Results are + also updated whenever you press Enter, and you can access previous + searches by pressing the 'Down' arrow or clicking the drop-down menu + icon at the side of the search box.
+You can sort results by clicking on the displayed columns, + and select entries with the mouse or keyboard. Once you have + selected one or more entries, hit the OK button to + retrieve the sequences.
human antigen |
- All entries containing both terms. | -
human AND antigen |
- |
human && antigen |
- |
"human antigen" |
- All entries containing both terms in the exact order. | -
human -antigen |
- All entries containing the term human
- but not antigen .
- |
-
human NOT antigen |
- |
human ! antigen |
- |
human OR mouse |
- All entries containing either term. | -
human || mouse |
- |
antigen AND (human OR mouse) |
- Using parentheses to override boolean precedence rules. | -
anti* |
- All entries containing terms starting with anti .
- Asterisks can also be used at the beginning and within terms. Note:
- Terms starting with an asterisk or a single letter followed by an
- asterisk can slow down queries considerably.
- |
-
author:Tiger* |
- Citations that have an author whose name starts with Tiger .
- To search in a specific field of a dataset, you must prefix your
- search term with the field name and a colon. To discover what
- fields can be queried explicitly, observe the query hints that are
- shown after submitting a query or use the query builder (see
- below).
- |
-
length:[100 TO *] |
- All entries with a sequence of at least 100 amino acids. | -
citation:(author:Arai author:Chung) |
- All entries with a publication that was coauthored by two - specific authors. | -
human antigen |
+ All entries containing both terms. | +
human AND antigen |
+ |
human && antigen |
+ |
"human antigen" |
+ All entries containing both terms in the exact order. | +
human -antigen |
+ All entries containing the term human
+ but not antigen .
+ |
+
human NOT antigen |
+ |
human ! antigen |
+ |
human OR mouse |
+ All entries containing either term. | +
human || mouse |
+ |
antigen AND (human OR mouse) |
+ Using parentheses to override boolean precedence + rules. | +
anti* |
+ All entries containing terms starting with anti .
+ Asterisks can also be used at the beginning and within
+ terms. Note: Terms starting with an
+ asterisk or a single letter followed by an asterisk can slow
+ down queries considerably.
+ |
+
author:Tiger* |
+ Citations that have an author whose name starts with
+ Tiger . To search in a specific field of a
+ dataset, you must prefix your search term with the field
+ name and a colon. To discover what fields can be queried
+ explicitly, observe the query hints that are shown after
+ submitting a query or use the query builder (see below).
+ |
+
length:[100 TO *] |
+ All entries with a sequence of at least 100 amino + acids. | +
citation:(author:Arai author:Chung) |
+ All entries with a publication that was coauthored by + two specific authors. | +
Result pagination
- The query results returned from the Uniprot server are paginated for performance optimisation. - The button labelled ' << ' and ' >> ' can be used to navigate to the next or previous result page respectively. - The page range is shown on the title bar of the Free Text Search interface. Jalview's pagination implementation supports multiple selection of entries across multiple pages. - - -- Customising The Uniprot Sequence Fetcher -
+ The query results returned from the UniProt server are paginated for + performance optimisation. The button labelled + ' << ' and + ' >> ' can be used to navigate to the + next or previous result page respectively. The page range is shown on + the title bar of the Free Text Search interface. Jalview's pagination + implementation supports multiple selection of entries across multiple + pages. + +- To change the displayed meta-data in the search result, click the - 'Customise Displayed Options' tab, and select the fields you'd like - to displayed or remove. + Customising The UniProt Sequence Fetcher
+To change the displayed meta-data in the search result, click + the 'Customise Displayed Options' tab, and select the fields you'd + like to be displayed or removed.
- The Uniprot Free Test Search Interface was introduced in - Jalview 2.9.1 + The UniProt Free Test Search Interface was introduced in + Jalview 2.10.0