</strong><em> Colours each residue in the structure with the colour
of its corresponding residue in the associated sequence as
rendered in the associated alignment views, including any
- Uniprot sequence features or region colourings.<br />Pick
+ UniProt sequence features or region colourings.<br />Pick
which of the associated alignment views are used to colour
the structures using the <strong>View→Colour
by ..</strong> sub menu.
</li>
</ol>
<p>
- If your DAS source selection contains sources which use Uniprot
- accession ids, you will be asked whether Jalview should find Uniprot
+ If your DAS source selection contains sources which use UniProt
+ accession ids, you will be asked whether Jalview should find UniProt
Accession ids for the given sequence names. It is important to
- realise that many DAS sources only use Uniprot accession ids, rather
- than Swissprot/Uniprot sequence names.<br> The <a
+ realise that many DAS sources only use UniProt accession ids, rather
+ than Swissprot/UniProt sequence names.<br> The <a
href="../webServices/dbreffetcher.html"
>database reference fetcher</a> documentation describes how Jalview
discovers what database references are appropriate for the sequences
</strong><em> Colours each residue in the structure with the colour
of its corresponding residue in the associated sequence as
rendered in the associated alignment views, including any
- Uniprot sequence features or region colourings.<br />Pick
+ UniProt sequence features or region colourings.<br />Pick
which of the associated alignment views are used to colour
the structures using the <strong>View→Colour
by ..</strong> sub menu.
</strong><em> Colours each residue in the structure with the colour
of its corresponding residue in the associated sequence as
rendered in the associated alignment view, including any
- Uniprot sequence features or region colourings.<br>
+ UniProt sequence features or region colourings.<br>
Residues which only exist in the PDB structure are coloured
white if they are insertions (relative to the associated
sequence in the alignment) and grey if they are N or C
<p>
Jalview can colour parts of a sequence based on the presence of
sequence features - which may be retrieved from database records
- (such as Uniprot), the result of <a href="search.html">sequence
+ (such as UniProt), the result of <a href="search.html">sequence
motif searches</a> or simply read from a <a href="featuresFormat.html">sequence
features file</a>. You can also <a href="creatinFeatures.html">create
features</a> from the results of searches or the current selection,
<p>
Since Jalview 2.08, sequence features assigned to a sequence can be
organised into groups, which may indicate that the features were all
- retrieved from the same database (such as Uniprot features), or
+ retrieved from the same database (such as UniProt features), or
generated by the same analysis process (as might be specified in a <a
href="featuresFormat.html"
>sequence features file</a>).
</p>
<p>If you use the WSDBFetch sequence fetcher services (EMBL,
- Uniprot, PFAM, and RFAM) in work for publication, please cite:</p>
+ UniProt, PFAM, and RFAM) in work for publication, please cite:</p>
<p>
Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate
J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez
correspondence between DNA and protein sequences. This mapping can
be imported directly from EMBL and EMBLCDS database records
retrieved by the <a href="seqfetch.html">Sequence Fetcher</a>, and
- allows sequence features to be mapped directly from Uniprot das
+ allows sequence features to be mapped directly from UniProt das
sources to their coding region on EMBL sequence records.
</p>
<p>In Jalview 2.9.1 <a href="siftsmapping.html">SIFTS Mapping</a> was added as a better means for explicitly identifying the coordinates corresponding to a displayed sequence when viewing a PDB structure associated with a sequence </p>
structures using various metric categories avaialble from the
meta-data of the structures. To perform this simply select any of the
following options from the drop-down menu in the Structure Chooser
- interface: Best Uniprot coverage, Higest Resolution, Best Quality,
+ interface: Best UniProt coverage, Higest Resolution, Best Quality,
Highest Protein Chain etc. When the 'Invert' option is selected,
Jalview returns an inverse result for the current selected option in
the drop-down menu.
<ul>
<li><strong>Fetch Sequence</strong><br> <em>Shows
a dialog window in which you can retrieve known ids from
- Uniprot, EMBL, EMBLCDS, PFAM, Rfam, or PDB database using
+ UniProt, EMBL, EMBLCDS, PFAM, Rfam, or PDB database using
Web Services provided by the European Bioinformatics
Institute. See <a href="../features/seqfetch.html">Sequence
Fetcher</a>
</p>
<ul>
<li><strong>Fetch Sequence</strong><br> <em>Shows a
- dialog window in which you can select known ids from Uniprot,
+ dialog window in which you can select known ids from UniProt,
EMBL, EMBLCDS, PDB, PFAM, or RFAM databases using Web Services
provided by the European Bioinformatics Institute. See <a
href="../features/seqfetch.html"
</ul></li>
<li><strong>Fetch Sequence<br>
</strong><em>Shows a dialog window in which you can select known ids
- from Uniprot, EMBL, EMBLCDS or PDB database using Web
+ from UniProt, EMBL, EMBLCDS or PDB database using Web
Services provided by the European Bioinformatics Institute.</em></li>
<li><strong>Save Project</strong><br> <em>Saves
all currently open alignment windows with their current view
</ul> <em>Application</em>
<ul>
<li><!-- JAL---></li>
+ <li><!-- JAL---></li>
+ <li><!-- JAL---></li>
+ <li><!-- JAL---></li>
+ <li><!-- JAL---></li>
+ <li><!-- JAL---></li>
+ <li><!-- JAL-2123 -->Show residue labels in Chimera when mousing over sequences in Jalview</li>
<li><!-- JAL-2027-->Support for reverse-complement coding regions in ENA and EMBL</li>
<li><!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2 for ENA record retrieval</li>
<li><!-- JAL 1812 -->New 'execute Groovy script' option in an alignment window's Calculate menu</li>
<a href="https://www.certum.eu">Certum</a> to the Jalview
open source project).
</li>
- <li>Jalview SRS links replaced by Uniprot and EBI-search
+ <li>Jalview SRS links replaced by UniProt and EBI-search
</li>
<li>Output in Stockholm format</li>
<li>Allow import of data from gzipped files</li>
current built in colourscheme is saved as new scheme</li>
<li>AlignFrame->Save in application pops up save
dialog for valid filename/format</li>
- <li>Cannot view associated structure for Uniprot sequence</li>
- <li>PDB file association breaks for Uniprot sequence
+ <li>Cannot view associated structure for UniProt sequence</li>
+ <li>PDB file association breaks for UniProt sequence
P37173</li>
<li>Associate PDB from file dialog does not tell you
which sequence is to be associated with the file</li>
<li>Save works when Jalview project is default format</li>
<li>Save as dialog opened if current alignment format is
not a valid output format</li>
- <li>Uniprot canonical names introduced for both das and
+ <li>UniProt canonical names introduced for both das and
vamsas</li>
<li>Histidine should be midblue (not pink!) in Zappo</li>
<li>error messages passed up and output when data read
due to null pointer exceptions</li>
<li>Secondary structure lines are drawn starting from
first column of alignment</li>
- <li>Uniprot XML import updated for new schema release in
+ <li>UniProt XML import updated for new schema release in
July 2008</li>
<li>Sequence feature to sequence ID match for Features
file is case-insensitive</li>
<li>Re-instated Zoom function for PCA
<li>Sequence descriptions conserved in web service
analysis results
- <li>Uniprot ID discoverer uses any word separated by
+ <li>UniProt ID discoverer uses any word separated by
∣
<li>WsDbFetch query/result association resolved
<li>Tree leaf to sequence mapping improved
<p>
<strong>The Sequence Identification Process</strong><br> The
method of accession id discovery is derived from the method which
- earlier Jalview versions used for Uniprot sequence feature retrieval,
- and was originally restricted to the identification of valid Uniprot
+ earlier Jalview versions used for UniProt sequence feature retrieval,
+ and was originally restricted to the identification of valid UniProt
accessions.<br> Essentially, Jalview will try to retrieve records
from a subset of the databases accessible by the <a
href="../features/seqfetch.html"
proteins can be retrieved via Jalview's new Ensembl REST client.</li>
<li><strong>Improved sequence/structure mappings.</strong>
Jalview now utilises the PDBe's SIFTS database (at EMBL-EBI) to
- match PDB data positions in Uniprot sequences.</li>
+ match PDB data positions in UniProt sequences.</li>
</ul>
</body>
git://source.jalview.org / jalview.git / commitdiff