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--$Revision: 1.28 $
--**********************************************************************
--
-- Definitions for CDD's
--
-- NCBI Structure Group
--
-- National Center for Biotechnology Information
-- National Institutes of Health
-- Bethesda, MD 20894 USA
--
-- October 1999
--
-- asntool -m cdd.asn -w 100 -o cdd.h
-- asntool -B objcdd -m cdd.asn -G -w 100 -I objseq.h objsset.h -K cdd.h \
-- -M asn.all
--**********************************************************************
NCBI-Cdd DEFINITIONS ::=
-- NCBI Conserved Domain Definition
BEGIN
EXPORTS Cdd-id, Cdd-id-set, Cdd, Cdd-set, Cdd-tree, Cdd-tree-set, Cdd-pref-nodes, Cdd-Project;
IMPORTS Date FROM NCBI-General
Pub FROM NCBI-Pub
Biostruc-annot-set FROM MMDB
Bioseq FROM NCBI-Sequence
Seq-annot FROM NCBI-Sequence
Seq-entry FROM NCBI-Seqset
Org-ref FROM NCBI-Organism
Seq-id FROM NCBI-Seqloc
Seq-interval FROM NCBI-Seqloc
Seq-loc FROM NCBI-Seqloc
Seq-feat FROM NCBI-Seqfeat
Score-set FROM NCBI-Seqalign
Cn3d-style-dictionary,
Cn3d-user-annotations FROM NCBI-Cn3d
PssmWithParameters FROM NCBI-ScoreMat;
-- dealing with lists of preferred tax-nodes
Cdd-org-ref ::= SEQUENCE {
reference Org-ref,
active BOOLEAN DEFAULT TRUE,
parent-tax-id INTEGER OPTIONAL,
rank VisibleString OPTIONAL
}
Cdd-org-ref-set ::= SET OF Cdd-org-ref
Cdd-pref-node-descr ::= CHOICE {
create-date Date,
description VisibleString
}
Cdd-pref-node-descr-set ::= SET OF Cdd-pref-node-descr
Cdd-pref-nodes ::= SEQUENCE {
preferred-nodes Cdd-org-ref-set,
model-organisms Cdd-org-ref-set OPTIONAL,
optional-nodes Cdd-org-ref-set OPTIONAL,
description Cdd-pref-node-descr-set OPTIONAL
}
-- Cdd's should not exist without a unique accession, but alternative id's may
-- be present as well. It is conceivable that a CD which is created as a merged
-- product of two highly redundant CDs will retain the source ids in addition
-- to its new unique id
Global-id ::= SEQUENCE {
accession VisibleString, -- SMART, Pfam, LOAD or CD accession
release VisibleString OPTIONAL, -- to hold CD-Database release number
-- if desired, currently not used
version INTEGER OPTIONAL, -- version 0 is the seed, version
-- numbers increase with update/curate
-- cycles
database VisibleString OPTIONAL -- this is NOT the source!, rather the
} -- database the object resides in
-- currently not in use
Cdd-id ::= CHOICE {
uid INTEGER, -- for synchronization with Entrez
-- holds PSSM-Ids
gid Global-id -- holds accession/version pairs
}
Cdd-id-set ::= SEQUENCE OF Cdd-id
Cdd-repeat ::= SEQUENCE { -- record whether the CD contains
-- repeated sequence/structure motifs
count INTEGER, -- number of tandem repeats in the CD
location Seq-loc OPTIONAL, -- location on the representative
avglen INTEGER OPTIONAL -- average repeat length
}
Cdd-book-ref ::= SEQUENCE { -- record a link to Entrez Books
bookname VisibleString, -- abbreviated book title
textelement ENUMERATED { unassigned(0), -- type of element
section(1), -- a section or paragraph
figgrp(2), -- a figure or set of figures
table(3), -- a table
chapter(4), -- a whole chapter
biblist(5), -- a lisf of references
box(6), -- an inserted box
glossary(7), -- glossary
appendix(8), -- appendix
other(255) },
elementid INTEGER OPTIONAL, -- numerical address of the text-element
subelementid INTEGER OPTIONAL, -- exact address, used with section
celementid VisibleString OPTIONAL, -- address of the text element, if character string
csubelementid VisibleString OPTIONAL -- exact address, if character string
}
-- The description of CDD's refers to the specific set of aligned sequences,
-- the region that is being aligned and the information contained in the
-- alignment. It may contain a lengthy comment
-- describing the function of the domain as well as its origin and all
-- other anecdotal information that can't be pressed into a rigid scheme.
-- Crosslinks to reference papers available in PubMed are possible as well.
-- There can be as many of these as you want in the CDD.
Cdd-descr ::= CHOICE {
othername VisibleString, -- alternative names for the CDD
-- if domain has several common names
category VisibleString, -- intracellular, extracellular, etc.
-- to record spatial and/or temporal
-- expression in free-text format
comment VisibleString, -- this is where descriptions go
reference Pub, -- a citation describing the domain
create-date Date, -- Date of first creation/dump
tax-source Org-ref, -- holds the highest common tax node
source VisibleString, -- the database the seeds were created
-- from, e.g. SMART, PFAM, etc..
status INTEGER { unassigned(0),
finished-ok(1), -- a public curated CD
pending-release(2), -- needs work done, not yet released
other-asis(3), -- imported as-is, immediate release
matrix-only(4), -- CD holds a Psi-Blast PSSM only,
-- does not contain alignment data
update-running(5), -- has been flagged for
-- update (in queue)
auto-updated(6), -- update finished, no
-- work necessary
claimed(7), -- is earmarked for curation
curated-complete(8),-- public curated member of a
-- completed family
other(255) }, -- for CD production?
update-date Date, -- Date of last version change
scrapbook SEQUENCE OF VisibleString, -- for storing curation notes
-- those won't make it into public
-- distributions
source-id Cdd-id-set, -- for linking back to source db
repeats Cdd-repeat, -- to record repeat counts
old-root Cdd-id-set, -- to record short-term history
curation-status INTEGER { unassigned(0), -- to record curation status
prein (1), -- when CD is checked out from
ofc (2), -- the tracking database, for
iac (3), -- use within curation software
ofv1 (4),
iav1 (5),
ofv2 (6),
iav2 (7),
postin (8),
other (255) },
readonly-status INTEGER { unassigned(0), -- to record read-only status
readonly (1), -- when CD is checked out from
readwrite (2), -- the tracking database, for
other (255) }, -- use within curation software
book-ref Cdd-book-ref, -- links to Entrez/books
attribution Pub, -- add citations and/or author names
title VisibleString -- hold short descriptive text
}
Cdd-descr-set ::= SET OF Cdd-descr
-- the Cdd-tree stores the hierarchy of CDDs. These objects are stored separate
-- from the CDs to allow for fast retrieval and use as an 'index' into CDs
-- all the components in a CD-tree match components in the full-sized CD
-- and should be synchronized
Cdd-tree ::= SEQUENCE {
name VisibleString, -- short name copied from CD
id Cdd-id-set, -- IDs copied from CD
description Cdd-descr-set OPTIONAL, -- description copied from CD
parent Cdd-id OPTIONAL, -- CD is the result of a split/merge
children Cdd-id-set OPTIONAL, -- this CD has been split
siblings Cdd-id-set OPTIONAL, -- related CDs (have common hits)
neighbors Cdd-id-set OPTIONAL -- co-occurring CDs (non-overlapping
-- hits to same sequences)
}
Cdd-tree-set ::= SEQUENCE OF Cdd-tree
-- Matrix definitions, these are supposed to store PSSMs and corresponding
-- matrices of relative residue frequencies.
-- the number of columns and rows is listed explicitly, values in columns
-- are stored column by column, i.e. in groups of nrows values for each column
Matrix ::= SEQUENCE {
ncolumns INTEGER,
nrows INTEGER,
row-labels SEQUENCE OF VisibleString OPTIONAL,
scale-factor INTEGER,
columns SEQUENCE OF INTEGER
}
-- definition for matrix of pairwise "distances", stored as the upper
-- triangle of a squared n x n matrix (excluding the diagonal), this is
-- supposed to store pairwise percentages of identical residues, pairwise
-- alignment scores or E-values from pairwise BLAST sequence comparisons
Triangle ::= SEQUENCE {
nelements INTEGER,
scores Score-set OPTIONAL,
div-ranks SEQUENCE OF INTEGER OPTIONAL
}
-- Update-align is supposed to contain alignments that still need some work
-- done to fit into the CD-proper alignment. These originate from the
-- CD update process (generated by Blast, for example) or may be created in
-- an editing session to save its state
Update-comment ::= CHOICE {
comment VisibleString, -- free text to describe nature of
-- Update-align
addthis Seq-loc, -- suggestion for inclusion in the CD
-- without corresponding alignment
replaces Seq-loc, -- if one or several alignment rows are
-- to be replaced by the Update-align
reject-loc Seq-loc, -- if used with Reject-id, specify a
-- location on a sequence which should
-- not be used
reference Pub -- if update alignment imported from
-- citation and for whenever it seems
-- necessary to cite
}
-- Both fields are optional, as the Update-align may be a Seq-annot without
-- description, or a suggestion to add a sequence without the corresponding
-- alignment
Update-align ::= SEQUENCE {
description SEQUENCE OF Update-comment OPTIONAL,
seqannot Seq-annot OPTIONAL, -- contains the SeqAlign
type INTEGER { unassigned(0),
update(1),
update-3d(2),
demoted(51),
demoted-3d(52),
other(255)}
}
Reject-id ::= SEQUENCE {
description SEQUENCE OF Update-comment OPTIONAL,
ids SET OF Seq-id
}
Feature-evidence ::= CHOICE {
comment VisibleString, -- so we can spell out what doesn't
-- fit in any other category
reference Pub, -- evidence via a literature reference
bsannot Biostruc-annot-set, -- evidence via Biostruc-features, such
-- as structure superpositions
seqfeat Seq-feat, -- evidence is a Sequence feature found
-- elsewhere
book-ref Cdd-book-ref -- evidence is a book chapter or figure
}
Align-annot ::= SEQUENCE {
location Seq-loc, -- points to a location in one of the
-- aligned sequences, usually the
-- master/representative
description VisibleString OPTIONAL, -- to hold descriptions/names like
-- "Heme binding site" or "catalytic
-- triad" etc., something that should
-- be used for labels in visualization
evidence SEQUENCE OF Feature-evidence OPTIONAL, -- evidence we can
-- compute with
type INTEGER OPTIONAL, -- for typing annotated features
-- 0 .. no type assigned
-- 1 .. active site
-- 2 .. polypeptide binding site
-- 3 .. nucleic acid binding site
-- 4 .. ion binding site
-- 5 .. chemical binding site
-- 6 .. posttranslational modification site
aliases SEQUENCE OF VisibleString OPTIONAL, -- adding more names for indexing
motif VisibleString OPTIONAL, -- to validate mapping of sites
motifuse INTEGER OPTIONAL -- 0 for validation,
-- 1 for motif somewhere in seqloc
-- 2 for multiple motifs in seqloc
}
Align-annot-set ::= SEQUENCE OF Align-annot
-- the Domain-parent records an evolutionary relationship which may not be
-- as simple as a classical parent-child relationship in a typical hierarchy,
-- i.e. where a CD is merely a specific subgroup ("child") of a more general
-- diverse alignment model ("parent"). A CD alignment model may be the result
-- of an ancient fusion event, combining two or more domains into a bigger unit
-- which has subsequently undergone a divergent evolutionary process similar to
-- what may have happened to a single "domain". A CD alignment model may
-- also reflect the result of a deletion event, where a specific subgroup
-- lacks part of a (set of) domain(s), but where the part present is found to
-- be highly similar to a putative "parent", with some added evidence for
-- an actual deletion, like from the distribution of truncated copies in phylogenetic
-- lineages. Deletion events which affect different parts of a set of
-- duplicated domain architectures may be indistinguishable from actual
-- fission events, which means that we may want to represent the latter as
-- deletions after duplication and do not need a special case for fissions.
Domain-parent ::= SEQUENCE {
parent-type INTEGER { classical (0), -- the classification of parent child relations
fusion (1),
deletion (2),
permutation (3),
other (255) },
parentid Cdd-id, -- identify the section parent by accession
seqannot Seq-annot OPTIONAL -- contains the sequence alignment linking
-- CD alignment models, should align the
-- masters/representatives of each CD
}
-- record sequence trees generated by a suitable algorithm.
Sequence-tree ::= SEQUENCE {
cdAccession VisibleString OPTIONAL,
algorithm Algorithm-type,
isAnnotated BOOLEAN DEFAULT FALSE,
root SeqTree-node
}
SeqTree-node ::= SEQUENCE {
isAnnotated BOOLEAN DEFAULT FALSE,
name VisibleString OPTIONAL,
distance REAL OPTIONAL,
children CHOICE {
children SEQUENCE OF SeqTree-node,
footprint SEQUENCE {
seqRange Seq-interval,
rowId INTEGER OPTIONAL
}
},
annotation Node-annotation OPTIONAL
}
Algorithm-type ::= SEQUENCE {
scoring-Scheme INTEGER { unassigned (0),
percent-id (1),
kimura-corrected (2),
aligned-score (3),
aligned-score-ext (4),
aligned-score-filled (5),
blast-footprint (6),
blast-full (7),
hybrid-aligned-score (8),
other (255) },
clustering-Method INTEGER { unassigned (0),
single-linkage (1),
neighbor-joining (2),
fast-minimum-evolution (3),
other (255) },
score-Matrix INTEGER { unassigned (0),
blosum45 (1),
blosum62 (2),
blosum80 (3),
pam30 (4),
pam70 (5),
pam250 (6),
other (255) } OPTIONAL,
gapOpen INTEGER OPTIONAL,
gapExtend INTEGER OPTIONAL,
gapScaleFactor INTEGER OPTIONAL,
nTerminalExt INTEGER OPTIONAL,
cTerminalExt INTEGER OPTIONAL,
tree-scope INTEGER { allDescendants (0),
immediateChildrenOnly(1),
selfOnly (2),
other (255) } OPTIONAL,
coloring-scope INTEGER { allDescendants (0),
immediateChildrenOnly (1),
other (255) } OPTIONAL
}
Node-annotation ::= SEQUENCE {
presentInChildCD VisibleString OPTIONAL,
note VisibleString OPTIONAL
}
-- the Cdd is the basic ASN.1 object storing an annotated and curated set of
-- alignments (formulated as a set of pairwise master-slave alignments).
-- The alignment data are contained in Seq-annots, and a special type of
-- object, the Update-align, contains additional alignment data from unfinished
-- editing sessions and update processes. The Biostruc-annot-set holds
-- structure superposition information for multiple structure-derived rows in
-- the alignment.
-- Version numbers in Global-ids are meant to be updated every time the Cdd is
-- changed in a way that does not require Global-ids to be changed (sequences
-- added in update cycle, annotation changed, alignment errors fixed)
Cdd ::= SEQUENCE {
name VisibleString, -- a short name (can be the accession..)
id Cdd-id-set, -- this CD's Ids
description Cdd-descr-set OPTIONAL, -- status, references, etc.
seqannot SEQUENCE OF Seq-annot OPTIONAL, -- contains the CD alignment
features Biostruc-annot-set OPTIONAL, -- contains structure
-- alignment data
-- or "core" definitions
sequences Seq-entry OPTIONAL, -- store as bioseq-set inside seq-entry
profile-range Seq-interval OPTIONAL, -- profile for this region only
-- also stores the Seq-id of the master
trunc-master Bioseq OPTIONAL, -- holds the truncated master, which
-- may be something like a consensus,
-- uses the same sequence coordinate
-- frame as the profile-range
posfreq Matrix OPTIONAL, -- relative residue frequencies
scoremat Matrix OPTIONAL, -- Position dependent score matrix
distance Triangle OPTIONAL, -- pairwise distances for all seqs.
parent Cdd-id OPTIONAL, -- this CD is the result of a split
children Cdd-id-set OPTIONAL, -- this CD has been split, not used
siblings Cdd-id-set OPTIONAL, -- related CDs (common hits), clusters
neighbors Cdd-id-set OPTIONAL, -- co-occurring CDs, not used
pending SEQUENCE OF Update-align OPTIONAL, -- contains alignments from
-- update or "lower panel"
rejects SEQUENCE OF Reject-id OPTIONAL, -- SeqIds of rejected CD-
-- members, ignore in update
master3d SET OF Seq-id OPTIONAL, -- record if CD has a 3D representative
alignannot Align-annot-set OPTIONAL, -- alignment annotation
style-dictionary Cn3d-style-dictionary OPTIONAL, -- record rendering styles
user-annotations Cn3d-user-annotations OPTIONAL, -- user annotations in Cn3D
ancestors SEQUENCE OF Domain-parent OPTIONAL, -- list of parents
scoreparams PssmWithParameters OPTIONAL,
seqtree Sequence-tree OPTIONAL
}
Cdd-set ::= SET OF Cdd
-- Cdd projects store a set of CDs, typically related to each other
-- relationships would be specified using the ancestors fields in the
-- individual CD objects. For use with CD-Tree, a program to visualize
-- curated CD hierarchies and evidence for hierarchical family structures.
Cdd-Viewer-Rect ::= SEQUENCE {
top INTEGER, -- top coordinate
left INTEGER, -- left coordinate
width INTEGER, -- width
height INTEGER -- height
}
Cdd-Viewer ::= SEQUENCE {
ctrl INTEGER { -- viewer type
unassigned (0),
cd-info (1),
align-annot (2),
seq-list (3),
seq-tree (4),
merge-preview (5),
cross-hits (6),
notes (7),
tax-tree (8),
dart (9),
dart-selected-rows (10),
other (255)
},
rect Cdd-Viewer-Rect OPTIONAL, -- viewer rectangle
accessions SEQUENCE OF VisibleString -- list of accessions associated with a viewer
}
Cdd-Script ::= SEQUENCE {
type INTEGER {
unassigned (0),
user-recorded (1),
server-generated (2),
other (255)
} OPTIONAL,
name VisibleString OPTIONAL, -- user assigned name/description
commands VisibleString -- actual script commands
}
-- cd colors are as: 0000FF for red, 00FF00 for green, FF0000 for blue
Cdd-Project ::= SEQUENCE {
cds SEQUENCE OF Cdd , -- cds
cdcolor SEQUENCE OF INTEGER, -- colors
viewers SEQUENCE OF Cdd-Viewer, -- Sequence viewers
log VisibleString, -- log
scripts SEQUENCE OF Cdd-Script OPTIONAL, -- command scripts
id Cdd-id-set OPTIONAL, -- to assign unique project id
rids SEQUENCE OF VisibleString OPTIONAL, -- to store request IDs for batch CD-Searches
create-date Date OPTIONAL,
update-date Date OPTIONAL,
project-id INTEGER OPTIONAL -- for temporary tracking in the database
}
END
|