RELEASE_NOTES.txt

OVERVIEW
--------

The genome_annotation service provides the following functionality to its clients:

    Gene calling via Glimmer and Prodigal.
    RNA calling via search_for_rnas.
    Special-protein calling (selenoprotein and pyrrolysoprotein).
    Determination of streptococcus repeat sequences.
    Protein annotation using the RAST kmer-based annotation algorithms.
    Metabolic reconstruction.
    Computation of close neighbors of a genome.

CHANGES - 2/26/2014
-------------------

Added the following command-line scripts (and associated API calls):

rast2-annotate-proteins-kmer-v1: Annotate CDS features using the SEED
FIGfam-based Kmers.

scripts/rast2-call-features-CDS-glimmer3: Call CDS features using glimmer.

rast2-call-features-ProtoCDS-kmer-v1: Call "proto-CDS" features from genome
DNA using the SEED FIGfam-based kmers.

rast2-call-features-ProtoCDS-kmer-v2: Call "proto-CDS" features from genome
DNA using the SEED function-based kmers.

rast2-export-genome: Export a genome object in a variety of formats.

CHANGES - 1/29/2014
-------------------

Added the following command-line scripts (and associated API calls):

rast2-call-features-CDS-prodigal: Call CDS features using the Prodigal gene
caller.

rast2-call-features-rRNA-SEED: Call rRNA features using code from the SEED project.

rast2-call-features-tRNA-trnascan: Call tRNA features using trnascan.

rast2-call-features-repeat-region-SEED: Call repeat region features using code
from the SEED project.

rast2-call-features-prophage-phispy: Call prophage regions using the phispy
application.

rast2-annotate-proteins-kmer-v2: Annotate CDS features using the SEED kmer
method.

rast2-export-genome: Export a genome object to a variety of standard output
formats.

CHANGES - 8/8/2013
------------------

At this point the module is generally stable, with no changes made in the recent past.