Getting started with HTJoinSolver

Loading IMGT Germlines

We are not authorized to redistribute IMGT® germline data. Therefore, users are required to download the germline genes themselves. We provide a simple mechanism for downloading the germlines. YOU ARE REQUIRED TO ABIDE BY ALL RESTRICTIONS PLACED BY IGMT. Please see http://www.imgt.org/Warranty.php. In particular:

Software material and data coming from IMGT server may be used for academic research only, provided that it is referred to IMGT®, and cited as "IMGT®, the international ImMunoGeneTics information system® http://www.imgt.org (founder and director: Marie-Paule Lefranc, Montpellier, France). For any other use please contact Marie-Paule.Lefranc@igh.cnrs.fr.

Assuming that you are authorized to do so, To download the germlines, select Download Germlines from IMGT under the Germlines menu. A popup window will allow you to enter a location to save the germlines. This downloads a fasta file from IMGT, and creates an XML file formatted appropriately for HTJoinSolver.

IMPORTANT: The first time you run the application, you must select Load Germlines from File under the Germlines menu. This actually reads the XML file created when you downloaded the germlines. You will only have to do this once, as HTJoinSolver will remember the location of the file.

After Selecting the Germlines, you can select the analysis type, and the species is listed as Homo sapiens, the source is also marked as IMGT.

If you want to update your germlines from IMGT, just repeat the download process and save the germlines in a different location. Do not try to save the germlines in the same file as the old germlines. In order to prevent excess load on the IMGT servers, we detect if the file is already downloaded. It will not overwrite an old file. After downloading the updated germlines, load the germlines from the new XML file.

Loading Custom Germlines

If you are not authorized to download IMGT germlines or would like to use your own custom germlines, you just need to provide the appropriate XML file. Please e-mail the corresponding author of the HTJoinSolver paper for assistance. We will provide more information online on create custom Germline datasources in the future. If you plan on maintaining and distributing the germlines, we can add a new menu item that loads your germlines in future versions of HTJoinSolver

Running HTJoinSolver

HTJoinSolver was designed to have a very simple interface for users. The input is a FASTA file of Ig gene sequences.  Clicking the "Select" button will bring up a file selection window.  The last couple FASTA files and output file are available in the pull down menu. You can quickly re-run analyses if needed. The output is an ms-excel formatted results file. Sorry, our collaborators really like excel. You have the ability to save the results as a comma, tab, or pipe (|) delimited file.  These file should make it easier for users of R or other statistical packages to import the results easier. You can also GZip the delimited files.  First select the delimiter, then select the GZip box.  Excel files can not be GZipped, if you select Excel, the Gzip is turned off.  R can read the GZipped results.

Creating FASTA files from a file of ACCESSION NUMBERS

If you have a file of accession number (1 accession number per line), Selecting create FASTA file from under the File menu will bring up a window that allows you to select your accession numbers and save the resulting FASTA file.  HTJoinSolver will look up the accession numbers in the NCBI nucleotide database.

Running HTJoinSolver on multicore machines

HTJoinSolver is a multithreaded application that can make use of multiple cores.  Under Advanced>Set Thread Count you can set the number of threads available for HTJoinSolver.  If you are the only person using a large machine, go ahead and set the number up to the number of cores on the machine (or close to it).  Setting the number of threads too high will hurt performance, so don't set it to more than the number of cores available to you.  By timing the application you can get an idea of the best number of threads to use.  This value is not saved, so every time you start HTJoinSolver don't forget to set it.

Setting the Submatrix/Scoring model

If you don't know what these are you should 1) read the HTJoinSolver paper 2) don't change them.  If you know what they are, it is easy to set under the Advanced menu.

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