A Quick Guide to Groove (G) allows you to draw IMGT Colliers de Perles IMGT/Collier-de-Perles After entering data related to an insertion into the for groove domains, including the G-DOMAIN of the fields ‘Position’, ‘Length’ and ‘Numbering labels’, press major histocompatibility (MH) proteins, and the G-LIKE- to the right of the amino acid insertion. http://www.imgt.org/3Dstructure-DB/cgi/Collier-de-Perles.cgi DOMAIN of MhcSF, other than MH. As a groove For more insertions, fill the information for the second comprises 2 G domains, the sequences of the two domains insertion, and repeat the procedure. To remove an insertion, for the IMGT Collier de Perles are entered in the same press the button next to the insertion you wish to page. remove. Number of Layers - the default value 1 depicts the 2D CDR3-IMGT length - enter the number of amino acids of representations of IMGT Collier de Perles on one layer; the CDR3-IMGT. selecting 2 depicts the 2D structure representation of Your Domain title 1 - enter the title for your graphical IMGT Collier de Perles on two layers, which is relevant representation of the given sequence (e.g., the name of the only for V and C domains. protein). CDR-IMGT colour type - select depending on the locus to which your sequence belongs. Domain Sequence 2 - this option is only available for This is a brief description of IMGT/Collier-de-Perles, Groove (G) domain type sequences. If you have selected the which is a part of IMGT®, the international 1 (IGH, TRB, TRD, RPI) displays the CDR-IMGT (or Groove (G) domain type at the corresponding field, the Immunogenetics Information System®. loops for RPI), with the Colour menu ‘red, orange, purple’ Domain sequence 2 option appears under the input fields of originally set up for the three CDR-IMGT of the VH the Domain sequence 1. Follow the same instructions as for IMGT/Collier-de-Perles is a 2D graphical representation domain of the IG heavy chains. the Domain Sequence 1 input fields. tool for protein domains. 2 (IGK, IGL, IGI, TRA, TRG) displays the CDR-IMGT This Quick Guide by no means replaces the documentation with the Colour menu ‘blue, green, green-blue’ originally To create the graphical representation of your sequence, available by IMGT. For full documentation on the software set up for the three CDR-IMGT of the VL domain of the press and the graphical representation will be created please visit: IG light chains. under the fields you filled in before. http://www.imgt.org Selecting 50% Hydrophobic positions at the Background http://www.imgt.org/3Dstructure-DB/doc/IMGTCollier-de- Background colour - select from the drop-down menu colour field and 1 (IGH, TRB, TRD, RPI), the result will Perles.shtml which property of your sequence you wish to highlight in resemble the representation below. the representation. ‘50% Hydrophobic positions’ is the The Collier de Perles tool can be found online at: default. http://www.imgt.org/3Dstructure-DB/cgi/Collier-de- Perles.cgi Domain Sequence 1 - in the available field, enter the sequence in FastA format, which you previously gapped with the IMGT/DomainGapAlign tool available at Domain Type - select one of the following depending on www.imgt.org/3Dstructure-DB/cgi/DomainGapAlign.cgi. the type of your domain: Examples of sequences in Fasta format can found at Variable (V) allows you to draw IMGT ‘Colliers de Perles’ www.imgt.org/3Dstructure- (pearl necklaces) for variable domains, including the V- DB/doc/IMGTDomainGapAlign_testsets.html DOMAIN of ImmunoGlobulins (IG) and T cell Receptors (TR), and the V-LIKE-DOMAIN of the Immunoglobulin Amino Acid insertions - this option is only needed if you Superfamily (lgSF), other than IG and TR. deal with unusual sequences characterised by insertions Constant (C) allows you to draw IMGT Colliers de Perles compared to the reference sequences. This can be the case for constant domains, including the C-DOMAIN of IG and for IgSF V-LIKE-DOMAIN that has amino acid insertions TR, and the C-LIKE-DOMAIN of the lgSF, other than IG compared to the IG and TR V-DOMAIN. and TR. The CDR-IMGT Colour menu ‘red, orange, purple’ is COPYRIGHT marked on the bottom of the schematic in the key: THIS DOCUMENT: was written and designed by Ioannis Bassis, Dimitrios Vlachakis, Patrice Duroux, Sophia Kossida, Marie-Paule Lefranc and is being distributed If you wish to highlight the CDR-IMGT of your sequence by the P&PR Project Committee of EMBnet. with the Colour menu ‘blue, green, green-blue’ (colour EMBnet - European Molecular Biology Network - is a menu for (IGK, IGL, TRA, TRG) the corresponding key world-wide bioinformatics support network. Most would be: countries have a national node which can provide training courses and other forms of help for users of bioinformatics software. For the same sequence as above, selecting IGH 80% You can find information about your national node from Hydropathy classes at the Background colour field will the EMBnet site: result in a representation like this. http://www.embnet.org/ A Quick Guide To IMGT/Collier-de-Perles First edition © 2014. Marie-Paule Lefranc. LICENSE: CC-BY-NC 3.0 http://creativecommons.org/licenses/by-nc/ A key appears on the right-hand-side of the schematic, showing which of the positions of the sequence are Hydrophobic, Neutral or Hydrophilic, and found with the same property (hydropathy class) in 80% or more of the VH domain sequences. Similarly, the choice made at the Background colour field, will highlight any other property (volume class, IMGT/Collier-de-Perles physicochemical class) you wish to highlight in the schematic. Positions with 45-degree hatch-lines represent IMGT gaps in the sequence. .