NESS: Vector-based Alignment-free Sequence Search
Project description
NESS
NESS is an alignment-free tool for sequence search based on word embedding. The tool is still under development and the code present in this repository is a proof of concept distributed under the GPL v3 license.
Usage
Currently the NESS CLI interface provides the following commands:
ness build_model
Creates a Word2Vec model from a multi FASTA file. For DNA sequences, use --both-strands
.
$ ness build_model \
--input swissprot.fasta \
--output swissprot.model
ness build_database
Similarly to makeblastdb
, formats a sequence database with vectors computed using a
model previously built. For DNA sequences, use --both-strands
.
$ ness build_database \
--input swissprot.fasta \
--model swissprot.model \
--output swissprot
ness search
Similarly to the blast*
programs, compares a multi FASTA file with the previously formated database.
$ ness search --input sequences.fasta --database swissprot --output hits.csv
Cite
Kremer, FS et al (2021). NESS: an word embedding-based tool for alignment-free sequence search. Available at: https://github.com/omixlab/ness.
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