From 9fb8dbc0e26d57a235a48b6f6054905e149dd169 Mon Sep 17 00:00:00 2001
From: jprocter
More information about the feature is given in a tooltip, which are +
More information about the feature is given in a tooltip, which is viewed by moving the mouse pointer over a sequence feature. The - associated text for the feature will then be displayed in a small - label will appear near the pointer.
+ description associated with the feature will then be displayed in a small + label near the pointer.After the Sequence Features option is selected, there may be some delay before - the features are actually rendered, as jalview must first determine if a - sequence is contained in uniprot and then retrieve its sequence - record. This delay should only happen once for a particular - alignment, as jalview caches uniprot records in a file in your home + the features are actually rendered, as jalview first determines if + the sequences are contained in Uniprot and then retrieves any sequence + records. This delay will normally only happen once for a particular + set of sequences, as jalview caches uniprot records in a file in your home directory called '.jalview.uniprot.xml'. -
The first step in this process is to try to use the ID (name) of - each sequence as an ID search in Uniprot. If there is no match, The - EBI Blast search is used in an attempt to obtain the Uniprot Id for - each sequence. You will be notified of any 100% matches with - Uniprot, but you must then manually change the name of the sequence, - by right clicking on the sequence ID and selecting - Sequence→Edit Name, before Jalview will show its sequence +
The Sequence Identification Process + +
+The first step in the procedure for matching uniprot IDs to + sequences is to use the ID (name) of + each sequence to retrieve Uniprot records directly.
++ If a uniprot record (or set of records) is found for a sequence, + then the sequence is aligned to the one in the Uniprot record + to determine the correct start and end residue positions (which are + displayed when the 'Show Full Sequence ID' option is set). +
+ +If the alignment reveals differences between the sequence in the + alignment and the one in the record, then Jalview will assume that + the aligned sequence is not the one in the uniprot record. + +
+ ++ In some cases, the ID used to retrieve Uniprot records may be out of + date and you will be notified of that a 100% match between the + sequence and a Uniprot record was identified, but the sequence name + must be manually changed (by right clicking on the sequence ID and selecting + Sequence→Edit Name), before Jalview will show its sequence features.
- If a uniprot record (or set of records) is found for a sequence, - then the sequence in aligned to the one in the Uniprot record - to determine the correct start and end residue positions that will be - displayed when the 'Show Full Sequence ID' option is set.