How does IgBLAST work?

IgBLAST has the capability to analyse nucleotide and protein sequences and can process sequences in batches. Furthermore, IgBLAST allows searches against the germline gene databases and other sequence databases simultaneously to minimize the chance of missing possibly the best matching germline V gene.

How do I download NCBI Blast database?

BLAST databases are updated daily and may be downloaded via FTP from ftp://ftp.ncbi.nlm.nih.gov/blast/db/. Database sets may be retrieved automatically with update_blastdb.pl, which is part of the BLAST+ suite. Please refer to the BLAST database documentation for more details.

What is antibody germline?

Antibody protein molecules are encoded by several recombined germline gene segments prior to antigen exposure. The initial set of antibodies that are generated by recombination in the bone marrow is the antigen-naïve antibody repertoire.

Is Blast an open source?

The BLAST program is based on an open-source format, giving everyone access to it and enabling them to have the ability to change the program code.

What is a germline sequence?

In biology and genetics, the germline is the population of a multicellular organism’s cells that pass on their genetic material to the progeny (offspring). In other words, they are the cells that form the egg, sperm and the fertilised egg.

What is K tuple in bioinformatics?

Word (k-tuple) methods. • Word methods, also known as k-tuple methods, are heuristic methods that are not guaranteed to find an optimal alignment solution, but are significantly more efficient than Smith- Waterman algorithm.

Is germline therapy legal?

Federal law prohibits the use of federal funds for research on human germline gene therapy. Germline gene editing is banned in the United States by acts of Congress although there is no federal legislation that dictates protocols or restrictions regarding human genetic engineering.

What is the igblast command line program?

There are two IgBlast command line programs, igblastn and igblastp. The former is for nucleotide sequences and the latter is for protein sequences. These examples assume that your current working directory has the following file structure after installation:

Where does igblastn program expect the internal_data directory?

Igblastn program expects the internal_data directory under current directory (i.e., where you run igblast program) or a path pointed to by IGDATA environmental variable (avoid using space in your path name for Windows system).

How do I search other databases with igblast?

Searching other databases in addition to germline database. Igblast allows you to search an additional database (such as NCBI nr database) as well as the germline database at the same time. You’ll get hits from the germline database followed by hits from the additional database.

Does igblast support custom organisms?

IgBLAST internally only supports organisms including human, mouse, rat, rabbit and rhesus_monkey. However, starting with version 1.16.0, IgBLAST also supports custom organism, although you need to prepare additonal files as follows. Make the germline V gene annotation file for your own organism.