AbFinder

Overview

AbFinder provides methods to mine large datasets of antibody sequences to rapidly identify sequences with high identity to known antibody sequences.

Given a MongoDB database and collection, AbFinder computes identity between one or more ‘standard’ sequences and all seqeunces in the collection. Default output is an identity/divergence plot, a hexbin plot of germline identity (X-axis) and identity to the standard sequence (Y-axis). AbFinder also updates MongoDB with identity information so that standard identities can be used in subsequent queries.

Examples

To run, AbFinder needs a MongoDB database and collection, an output directory, and a FASTA-formatted file of standard sequences:

$ abfinder -d MyDatabase -c MyCollection -s standards.fasta -o /path/to/output/

Omitting the collection results in AbFinder iteratively processing each collection in the database. By default, AbFinder assumes that the standard file contains amino acid sequences. If you would like to compute nucleotide identity instead, you can indicate your preference with the --nucleotide option:

$ abfinder -d MyDatabase -s standards.fasta -o /path/to/output/ --nucleotide

AbFinder also assumes that the standard file contains heavy chain sequences, and only heavy chain sequences from MongoDB will be used for comparison. To compare sequences of a different chain (options are 'heavy', 'kappa', and 'lambda'), use the --chain option:

$ abfinder -d MyDatabase -s standards.fasta -o /path/to/output/ --chain kappa

If you do not plan on using the identity scores for any sort of downstream analysis, you can save some time and skip the MongoDB updates and just make the identity/divergence figures:

$ abfinder -d MyDatabase -s standards.fasta -o /path/to/output/ --no-update

There are several other options, mainly related to formatting the identity/divergence figures. A complete list of all options can be obtained with:

$ abfinder --help