v0.2.16

PROST v0.2.16

Fix warning about regex patterns.

Add split option to makedb command that splits large protein databases into chunks.

• prost.py makedb -s 1000 input.fa output will split input.fa into 1000 proteins and create output_0.prdb, output_1.prdb so on and so forth.
• prost.py mergedbs output_* merged.prdb will merge smaller databases into one big database

v0.2.15

PROST v0.2.15

Rename prost script as prost.py so that it works in Windows.

v0.2.13

PROST v0.2.13

• You can parallelize the PROST search by using the --jobs option.

v0.2.9

PROST v0.2.9

• searchsp command now produces results in JSON format which is usable with the JSONWP tool. This allows visualization of results in a browser. A table is generated that contains all the query proteins in the search. For each query protein, a page is created that contains GO annotation enrichment results and putative homologs found by PROST. For each putative homolog found, there is an alignment page that shows the Alphafold 2 structures if available and sequence alignment that is produced using the PROTSUB matrix.

v0.2.8

PROST v0.2.8

• Update SwissProt database to February 2023 Release
• Add GO annotation enrichment analysis to searchsp command
• Use Github for PROST file hosting

v0.2.7

PROST v0.2.7

• Update SwissProt database to February 2023 Release
• Add GO annotation enrichment analysis to searchsp command
• Use Github for PROST file hosting

v0.2.6

PROST v0.2.6 Release

• Fix wrong command name bug
• Add --no-cache argument to the makedb command which disables recalling embeddings from the cache.

v0.2.5

PROST v0.2.5 Release

• Added GPU embedding support
• Added prostDistance function and example script

v0.2.1

Prost v0.2.1 release

The first working release of the PRotein Ortholog Search Tool (PROST) package.

Features

• Protein database creation and search
• SwissProt database search