CaBLASTP is a suite of homology search tools, powered by
compressively-accelerated protein BLAST (CaBLASTP), which are
significantly faster than and comparably accurate to all known state-of-
the-art tools including HHblits, DELTA-BLAST, and PSI-BLAST.
Further, our tools are implemented in a manner that allows direct
substitution into existing analysis pipelines. The key idea is that we
introduce a local similarity-based compression scheme that allows us
to operate directly on the compressed data. Importantly, CaBLASTP's
runtime scales almost linearly in the amount of unique data, as
opposed to current BLASTP variants which scale linearly in the size of
the full protein database being searched. Our compressive algorithms
will speed up many tasks such as protein structure prediction and
orthology mapping which rely heavily on homology search.
Source code, binaries, and a compressed NCBI NR database are available here:
Note: if you wish to install from source, we do not recommend downloading the
source code from here. Instead, install Go and
run "go get github.com/BurntSushi/cablastp/...". More details are in the README file.