CDD preview data directory     README file, revised 27 May 2025
===============================================================================
https://ftp.ncbi.nlm.nih.gov/pub/mmdb/cdd/preview/README

This directory contains data files that give a preview of the next/upcoming 
Conserved Domain Database release. It will be updated several times a year and
is not guaranteed to exactly correspond to a particular CDD release.

Files are:

-------------------------------------------------------------------------------
FILE NAME                     | summary 
-------------------------------------------------------------------------------
Cdd_preview.tar.gz            | the cdd_preview RPS-BLAST search database, pre-
                              | formatted
-------------------------------------------------------------------------------
acd.tar.gz                    | CD data as used by the CD-server for 
                              | visualization of CD-search results
                              | (scope A, PLUS data for superfamily clusters)
-------------------------------------------------------------------------------
bitscore_specific_preview.txt | domain-specific score thresholds used by 
                              | CD-Search tool to determine whether hits to
                              | NCBI-curated domain models are specific or 
                              | non-specific
-------------------------------------------------------------------------------
cdd.info                      | CDD release version number and details
-------------------------------------------------------------------------------
cdd.tar.gz                    | PSSMs originating from various alignment
                              | collections; can be used to build search
			      | databases for RPS-BLAST. 
-------------------------------------------------------------------------------
cdd.versions                  | list of all conserved domain model accessions,  
                              | versions, and PSSM IDs present in the current
			      | and previous versions of the Conserved Domain
			      | Database 
-------------------------------------------------------------------------------
cddannot.dat.gz               | information about conserved family features
                              | (such as binding and catalytic sites) as  
                              | recorded for NCBI-curated CD models
-------------------------------------------------------------------------------
cddannot_generic.dat.gz       | information about generic conserved family
                              | features (such as binding and catalytic sites)
			      | in root CD models that can be mapped to all 
			      | hierarchy members.
-------------------------------------------------------------------------------
cddid.tbl.gz                  | summary information about the CD models in this
                              | distribution that are part of the 
                              | "cdd_preview" database  
-------------------------------------------------------------------------------
cddid_all.tbl.gz              | summary information about all CD models in this 
                              | distribution 
-------------------------------------------------------------------------------
cddmasters.fa.gz              | FASTA-formatted sequences that show
                              | representative sequences for each conserved
                              | domain model in the collection
-------------------------------------------------------------------------------
cdtrack.txt                   | information from NCBI's internal tracking
                              | system about hierarchies of related domain
			      | models in 
-------------------------------------------------------------------------------
fasta.tar.gz                  | sequence alignments from the CDs in mFASTA
                              | format
-------------------------------------------------------------------------------
README                        | this file
-------------------------------------------------------------------------------

In order to use the CDD preview dataset together with the rpsbproc package, you
will need to substitute the rpsbproc datafiles with those downloaded from the 
preview directory. See

https://ftp.ncbi.nlm.nih.gov/pub/mmdb/cdd/rpsbproc/README

for instructions on how to set up and use rpsbproc. The rpsbproc command line 
utility is an addition to the standalone version of Reverse Position-Specific
BLAST (RPS-BLAST), also known as CD-Search (Conserved Domain Search). 
rpsbproc facilitates formatting/annotation of standalone rpsblast search 
results to provide a richer source of information including
 - characterization of conserved domain hits as specific (crossing a score 
   threshold set for each model) or superfamily-level
 - annotation of functional sites on the user-provided query sequence, as 
   recorded with NCBI-curated conserved domain models
   
The file "bitscore_specific_preview.txt" will have to be renamed to 
"bitscore_specific.txt" for use with rpsbproc