Performing a Query
The database can be searched according to germline gene usage, clinical categories,
and various identifiers.
Germline Gene Usage
These options represent the variable region germline gene usage, organized by family.
All genes are specified using the IMGT nomenclature.
Clinical Category
Sequences in the database are divided into three main categories.
- AL-PCD: Plasma Cell Dyscrasia (PCD) and AL Amyloidosis.
- Other PCD: This includes other PCD's such as Multiple Myeloma and Light Chain Deposition Disease.
- Non-PCD: All other LC sequences, including normal repertoire, autoimmune, and anti-infectious LCs.
Identifiers
Please separate accession numbers or clone/isolate/patient ID's by spaces.
Sample Sources
Sequences can be searched by their molecule type, cell type, and tissue type, when specified.
Query Results
The results page presents the set of sequences that matches your query.
20, 50, 100, or 1000 sequences can be shown at one time.
Sequences can be sorted by accession number, patient ID, or germline gene usage (variable, joining, constant).
Germline gene names are given using their IMGT gene name (IGKV1-12) and allele (*01).
Click on an accession number to learn more about that sequence.
Selection
Next to each sequence is a check box. Selected sequences can be aligned, removed from the current set,
or downloaded using the buttons at the bottom of the page.
Alignments
The alignments page shows an alignment for sequences selected by a search. All alignments
are presented using the
IMGT numbering.
Type
Choose a protein or nucleotide alignment for the selected sequences.
Header line
Each row of an alignment has a header line at top that displays the sequence position.
This row is colored according to the IMGT region at that position. Framework (FR) and Constant (C) regions
are colored
light grey, and Complementarity Determing Regions (CDR) are colored
dark grey.
Color by Residue
Assigns each residue a color according to several color menus for Immunoglobulin sequences from the IMGT.
A full description is available
here.
11 IMGT amino acid chemical characteristics classes
- Aliphatic
- Phenylalanine
- Sulfur
- Glycine
- Hydroxyl
- Tryptophan
- Tyrosine
- Proline
- Acidic
- Amide
- Basic
7 IMGT amino acid chemical characteristics classes
- Aliphatic
- Phenylalanine/Sulfur
- Glycine/Hydroxyl/Tyrosine
- Tryptophan
- Proline
- Acidic/Amide
- Basic
5 IMGT amino acid volume classes
- 60-90
- 108-117
- 138-154
- 162-174
- 189-228
3 IMGT amino acid hydropathy classes
- Hydrophobic
- Neutral
- Hydrophilic
Color by Property
Additionally, sequences can be colored according to a small set of amino acid properties from the
Amino acid indices and similarity matrices Database (AAindex).
Each property
is scaled to a [-1,1] interval and these values are converted to colors, with blues representing
the low values and reds the high ones.
| -1 |
-0.75 |
-0.5 |
-0.25 |
0 |
0.25 |
0.50 |
0.75 |
1 |
| |
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|
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The current set of properties are:
URD980101 Modified Kyte-Doolittle hydrophobicity scale (Juretic et al., 1998)
BHAR880101 Average flexibility indices (Bhaskaran-Ponnuswamy, 1988)
PONJ960101 Average volumes of residues (Pontius et al., 1996)
JANJ780101 Average accessible surface area (Janin et al., 1978)
ZIMJ680104 Isoelectric point (Zimmerman et al., 1968)
BEGF750102 Conformational parameter of beta-structure (Beghin-Dirkx, 1975)
Regions
It is possible to align and view certain regions according to the IMGT standardized numbering.
These regions are:
- V-REGION
- V-J-REGION
- V-J-C-REGION
- JUNCTION (not yet available)
- CDR1-IMGT
- CDR2-IMGT
- CDR3-IMGT
- FR1-IMGT
- FR2-IMGT
- FR3-IMGT
- FR4-IMGT
- C-REGION (not yet available)
Download Alignment
Click 'download' on the alignment page to download the currently viewed alignment.
Currently, the only available format is CLUSTALW.