Commit d2dbacf1 authored by marc duez's avatar marc duez Committed by Mathieu Giraud
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user.md : aligner

description des menus de l'aligner
parent 3978e689
......@@ -237,35 +237,73 @@ or their “N length” (that is N1-D-N2 in the case of VDJ recombinations).
## The sequence panel (bottom panel)
The sequence panel displays nucleotide sequences from selected clones.
Nucleotide or amino acid sequences of selected clones can be inspected using the Sequence panel.
- See "[What is the sequence displayed for each clone ?](#what-is-the-sequence-displayed-for-each-clone)" below
- Sequences can be aligned together (“align” button), identifying substitutions, insertions and deletions. Silent mutations are identified, as soon as a CDR3 is detected, and represented with a double border in blue.
- You can remove sequences from the aligner (and the selection) by clicking on the “X” at the left.
- You can unselect all sequences by clicking on the background of the grid.
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.
## Further sequence analysis with external software
The sequence panel displays buttons to further analyze the selected sequences
with other software useful for RepSeq studies.
These buttons open another window/tab.
### 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 .scatterplot using a click-and-drag to select multiple clones at the same time.
- 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.
- [`❯ IMGT/V-QUEST`](http://www.imgt.org/IMGT_vquest):
The reference analysis from IMGT®, including subset #2 and #8 search.
The `▼` button further allows to retrieve back results from IMGT/V-QUEST
and to display them within Vidjil.
The first sequence selected is often used as the reference when further inspecting the
- [`❯ IgBlast`](https://www.ncbi.nlm.nih.gov/igblast/):
Nucleotide alignment with IG/TR germline sequences
## Using the sequence panel tools
- `❯ CloneDB`. See [above](#detailed-information-from-clonedb)
At the top of this panel you can find a menu providing multiple tools to inspect the sequences, that are in order:
- [`❯ Blast`](http://www.ensembl.org/Multi/Tools/Blast):
Nucleotide alignement against the Homo sapiens genome and other nucleotide collections
### 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.
- [`❯ AssignSubsets`](https://station1.arrest.tools/subsets) (availaible for clones with IGH recombinations):
Assignment to the [19 known major subsets](https://www.ncbi.nlm.nih.gov/pubmed/22415752)
of stereotyped antigen receptor sequences for CLL
### 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 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 is
### External Analysis: Further sequence analysis with external software
This sub menu display a range of other analysis software available online used for RepSeq studies.
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.
- [`❯ IgBlast`](https://www.ncbi.nlm.nih.gov/igblast/):
Nucleotide alignment with IG/TR germline sequences
- `❯ CloneDB`. See [above](#detailed-information-from-clonedb)
- [`❯ Blast`](http://www.ensembl.org/Multi/Tools/Blast):
Nucleotide alignement against the Homo sapiens genome and other nucleotide collections
- [`❯ AssignSubsets`](https://station1.arrest.tools/subsets) (availaible for clones with IGH recombinations):
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
- 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.
- V/D/J Genes
- FR1/FR2/FR3
- 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.
# The sample database and the server
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