Commit 6f0ba205 authored by Mathieu Giraud's avatar Mathieu Giraud
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doc/user.md: sequence panel, rework and details

parent 62457ed3
......@@ -237,49 +237,50 @@ or their “N length” (that is N1-D-N2 in the case of VDJ recombinations).
## The sequence panel (bottom panel)
Nucleotide or amino acid sequences of selected clones can be inspected using the Sequence panel.
The sequence panel shows, for the selected clones:
We invite you to read "[What is the sequence displayed for each clone ?](#what-is-the-sequence-displayed-for-each-clone)" below before using this tool.
- the nucleotide or amino acid *sequences* -- see below "[What is the sequence displayed for each clone ?](#what-is-the-sequence-displayed-for-each-clone)"
- some *features* on these sequences
### Select clones to inspect
- Select a single clone : click on it's representative element in any panel. (it can be a plot in the gridpanel, a line in the graph panel or an entry in the list panel)
- Select multiple clone : it's possible to do a rectangular selection of an area of the grid panel using a click-and-drag to select multiple clones at the same time.
### Selecting clones for inspection
Clones can be (un)selected by several ways:
- Select one clone: click on its representative element in any panel (a plot in the gridpanel, a line in the graph panel, or an entry in the list panel)
- Select multiple clones at once: click-and-drag a rectangular selection of an area of the grid panel
- Add a clone to the selection : Ctrl+click
- Remove a clone from the selction : click on the 'X' at the left.
- Remove all selected clone : click on the background of the grid.
- Remove a clone from the selection : click on the 'X' at the left
- Remove all selected clones : click on the background of the grid panel
The first clone selected is often used as the reference when further inspecting the sequences
### Cluster: regroup clones
## Using the sequence panel tools
The `cluster` button will create a cluster with the selected clones
Such a cluster will appear as a single clone,
with the first (largest) selected clone acting as its representative.
At the top of this panel you can find a menu providing multiple tools to inspect the sequences, that are in order:
### Align
### Cluster: regroup clones
This button will create a cluster with the selected clones
a cluster of clones will appear like a single clone in the application with the first selected clone acting as it's representative.
The `align` button aligns all the selected sequences,
the sequence of the first (largest) clone used as a reference.
### Align:
provide an alignement of the sequences, the sequence of the first clone in the list is used as the reference and all the other sequences are aligned against it.
by default
- `*` is a match
- `-` is a gap
- a single line under a character is a nucleotide mismatch
- a double line under a character is a silent nucelotide mismatch (not impacting the resulting amino acid sequence)
- `#` in an amino acid sequence indicates a frameshift in the junction (and thus an unproductive sequence)
- `-` is a gap.
- `*` is a match.
- a single line under a character is a mismatch.
- a double line under a character is a mismatch that does not impact the resulting amino acid sequence.
- `#` in an Amino acid sequence indicate a frameshift in the junction.
The alignment settings `⚙` menu allows to customize such alignements, by
look at the available options available in the sub-menu "[Alignement Settings](### Alignement settings)" below to see how to customize.
- highlighting mismatches
- hiding matches
- switching between amino acid and nucleotide sequences
### Data Colums
Every clone can have a lot of different available data depending on the analysis software used for the processing, use this menu to select which data you want to be displayed alongside the clone name.
### Alignement settings
Customize the alignement display
### Data Columns
- highlight mismatch
- hide match
- switch between Amino Acid and nucleotidic sequence
The analysis software, on some configurations, may provide additional data for each clone.
The data columns `‖` menu allows to select such data.
### External Analysis: Further sequence analysis with external software
......@@ -287,7 +288,8 @@ This sub menu display a range of other analysis software available online used f
These buttons will send the sequences of selected clones to them for analysis and open the resulting page in another window/tab.
- [`❯ IMGT/V-QUEST`](http://www.imgt.org/IMGT_vquest):
The reference analysis from IMGT®, including subset `#2` and `#8` search.
The reference analysis from IMGT®, including search for subset `#2` and `#8`.
See [below](#imgt-sequence-features)
- [`❯ IgBlast`](https://www.ncbi.nlm.nih.gov/igblast/):
Nucleotide alignment with IG/TR germline sequences
......@@ -301,21 +303,25 @@ These buttons will send the sequences of selected clones to them for analysis an
Assignment to the [19 known major subsets](https://www.ncbi.nlm.nih.gov/pubmed/22415752)
of stereotyped antigen receptor sequences for CLL
### Sequence Feature
The analysis software can sometime provide positions of genes or specific regions that can be highlighted using this menu.
The content of his menu depends on the analysis software(and parameter) used but usually contains at least the following genes/regions
### Sequence Features
Depending on the analysis software and on its configuration, there can be positions of genes or specific regions of interest that can be highlighted.
The sequence feature `☰` menu usually contains at least the following genes/regions:
- V/D/J Genes
- V/D/J genes
- CDR3 position
### Sequence Feature `IMGT`
Same as Sequence Feature but this time the information that can be displayed are provided by IMGT/V-QUEST online analysis software.
### IMGT Sequence Features
The `☰ IMGT` menu further allows to select features provided by IMGT/V-QUEST:
- V/D/J Genes
- FR1/FR2/FR3
- V/D/J genes
- FR1/FR2/FR3/FR4
- CDR1/CDR2/CDR3
It is required to use the refresh button after adding new clones to the selection to avoid overloading the IMGT servers that provide us this feature.
To avoid overloading the IMGT servers that provide us this feature,
after adding new clones to the selection,
one has to click on the refresh `↻` button to request the features for the new sequences.
# The sample database and the server
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