Commit f98ac893 authored by Mathieu Giraud's avatar Mathieu Giraud
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Merge branch 'doc/external-software' into 'dev'

Doc/external software

See merge request !645
parents 764b1eb2 1e7df835
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......@@ -142,7 +142,9 @@ e-value, number of reads) about each clone.
In addition, depending on what the user launched on this clone, we may also
find detailed informations retrieved from IMGT or from CloneDB.
#### Detailed information from CloneDB (experimental feature)
#### Detailed information from CloneDB
(experimental feature)
If you are connected to a patient/experiment database where CloneDB is enabled,
and if CloneDB was launched on the selected clone,
you can see here occurrences of this clone in CloneDB
......@@ -207,9 +209,32 @@ The sequence panel displays nucleotide sequences from selected clones.
- 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 further analyze the sequences with IMGT/V-QUEST, IgBlast or Blast. This opens another window/tab.
- You can unselect all sequences by clicking on the background of the grid.
## 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.
- [`❯ IMGT/V-QUEST`](http://www.imgt.org/IMGT_vquest):
The reference analysis from IMGT®.
The `▼` button further allows to retrieve back results from IMGT/V-QUEST
and to display them within Vidjil.
- [`❯ 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`](http://tools.bat.infspire.org/arrest/assignsubsets/) (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
# The patient/experiment database and the server
If a server with a patient/experiment database is configured with your
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