The blast database files need to be put under internal_data/my_organism folder (for example internal_data/sheep). Make sure you use the -parse_seqids flag when using makeblastdb. This database needs to be named my_organism_V (for example sheep_V). Make a blast sequence database for germline V genes that correspond to what you have annotated above. Note that you do not need to make annotations for all alleles of a V gene. If you use the Kabat numbering system, the file must be named my_ or my_. For annotations using the IMGT numbering system, the file must be named my_ for igblastn (for example ) or my_ for igblastp (for example ). This file must be put under the internal_data/my_organism folder (for example internal_data/sheep). The purpose of this file is to provide information such as CDR/FWR regions for your germline V genes (see internal_data/human/ for an example). Make the germline V gene annotation file for your own organism. However, starting with version 1.16.0, IgBLAST also supports custom organism, although you need to prepare additonal files as follows. IgBLAST internally only supports organisms including human, mouse, rat, rabbit and rhesus_monkey.
Procedure to set up IgBLAST for custom organism You can directly supply a path to this file or put it under a path pointed to by IGDATA environmental variable. You need to use -auxiliary_data option to specify your file. If you search your own database and if it contains different sequences or sequence identifiers, then you need to edit the corresponding file accordingly (Enter -1 if the frame information is unknownor) or you won’t get proper frame status or CDR3 information (other results will still be shown correctly). The suppliled annotation information is only for NCBI or IMGT germline gene sequence database (including gene names as well as the sequences). The optional_file directory contains files that indicate germline J gene coding frame start position (position is 0-based), the J gene type, and the CDR3 end position for each sequence in the germline J sequence database (Fields are tab-delimited). Note that this directory does NOT contain any germline gene databases you should search (see aboveįor how you can obtain a germline gene database). Program) or a path pointed to by IGDATA environmental variable (avoid using space in your path name for Igblastn program expects the internal_data directory under current directory (i.e., where you run igblast The internal_data directory contains data internal to igblast program only and users should NEVER add, delete, move, copy or edit any files in this directory.
Now you can use my_seq_file as blast database file for IgBlast. For example:īin/makeblastdb -parse_seqids -dbtype nucl -in my_seq_file After you have downloaded the sequences, invoke our utility tool edit_imgt_ (in the bin directory in the IgBlast release package) to process these sequences (i.e., to change the long IMGT definition lines to germline gene names only). Combine all V, all D and all J sequences, respectively, into separate files (i.e., one file for all V sequences, one for all D sequences and one file all for J sequences).
Rat tool for mac download#
You need to download all V, D and J sequences for whatever organisms you are interested in.
To search IMGT germline sequences, you need to download them from IMGT web site The NCBI mouse germline gene databases (i.e., mouse_gl_V, etc.) are supplied on our ftp site (. IgBlast allows you to search any germline databases of your choice (using -germline_db_V, -germline_db_J and -germline_db_D options). Get blast database for germline V, D, and J gene sequences. We strongly encourage you to get the latest IgBlast version with built-in internal_data and optional_file. Note, for versions prior to 1.13.0 only, you also need to download the old internal_data and optional_file folders from.
Rat tool for mac code#
We provide pre-compiled programs for Linux, Windows, MacOs as well as source code for you to build on your own platform. IgBlast program can be downloaded from ( ).
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