Clone DB Help

  1. Introduction
  2. Library Browsers
  3. Library Records
  4. Clone Records
  5. CloneDB Entrez Search

1. Introduction

The NCBI Clone DB replaces and expands upon the former NCBI Clone Registry, which was established during the era of the human and mouse genome projects, to now represent a broader range of eukaryotic organisms and clone types. Clone DB integrates information about clones and libraries, including sequence data, map positions and distributor information. This consolidation provides for a more comprehensive view of clone-associated data that will help users take greater advantage of clone resources. Currently, Clone DB contains data associated with genomic and cell-based (e.g. gene trap, gene targeting) clones.

Clone DB is a free resource that is developed and maintained by the National Center for Biotechnology Information (NCBI), at the U.S. National Library of Medicine (NLM), located at the National Institutes of Health (NIH) in Bethesda, Maryland.


2. Library Browsers

Data in Clone DB is organized by library, and all clones belong to a library. All libraries in Clone DB have been externally defined, either by the library creator or distributor. The Clone DB library browsers provide a summary of clone libraries with records in the database. Genomic libraries may be viewed in the genomic library browser (Figure 1), while cell-based libraries can be viewed in the cell-based library browser (Figure 2). Data in the browsers can be sorted by any of the table columns. In addition, both browsers can be filtered to restrict the display to libraries meeting specific criteria. Detailed records for each of the libraries are available by clicking on the library name or abbreviation in this browser.

Figure 1. Genomic Library Browser

genomic browser

Figure 2. Cell-Based Library Browser

cell-based browser


3. Library Records

Each library in Clone DB has a record page that displays basic information about the library's features. These records can be accessed by clicking on the library names in either the genomic or cell-based library browsers. At the top of each library record page is a summary section providing key information about the library, such as its name, its type and the organism it represents. Links to publications describing the library's construction are provided, as are links to the organism-specific pages in the NCBI BLAST and MapViewer pages, and to BioProject, if the library was used for such a purpose. Mouse cell-based library records include a link to MGI, the source of the library data. Distributor information is provided in the library summary for genomic library records. However, because individual clones from cell-based libraries may be available in various formats from different distributors, Clone DB provides distributor information for cell-based clones as part of the individual clone record. The library summary is followed by a Library Details section, where users can find information about DNA source, construction, statistics, host, and alternate names and/or abbreviations by which the library is known.

Figure 3a. Genomic Library Record: Summary and DNA Source Tab. In addition to summary information, the library record provides links to the PubMed records of publications describing the library construction. In addition, summary information is provided for library construction publications not in the PubMed database. Links are provided to organism-specific pages for BLAST, MapViewer and Clone Finder, as well to any BioProject records associated with the library. The DNA Source tab provides information about the organism from which the DNA used to construct the library is derived, when such information is available.

gen lib record summary


Figure 3b. Genomic Library Record: Library Construction Tab. This tab provides information about the construction of the library, such as the cloning vector and cloning sites.

gen lib record construction


Figure 3c. Genomic Library Record: Library Statistics Tab. The library statistics tab provides statistics such as average insert size and standard deviation, library coverage, plate ranges and the percent of non-recombinant or contaminated clones.

gen lib record statistics


Figure 3d. Genomic Library Record: Alternate Library Names Tab. This tab lists alternative names and abbreviations by which the library may be publicly known.

gen lib record altnames


Figure 3e. Cell-Based Library Record: Summary and Library Construction Tab. The library construction tab for cell-based libraries provides the name of the library creator, as well as the vector used.

cell-based lib record summary


Figure 3f. Cell-Based Library Record: Library Host Tab.The library host tab provides information about the material in which the cell-based library was constructed. This includes the name of the parental cell line and its strain of origin.

cell-based lib record host


4. Clone Records

The Clone DB clone record page displays information specific to that clone. At the top of the page is a section with general information about the clone, such as the name by which it's known in Clone DB, any aliases, the organism it represents, a link to its library record page, and the library type. There is also an ideogram showing the clone's location on the genome, if this has been determined. The clone summary is followed by a tabbed section that contains additional clone details, if known. These include: placement information, associated sequences, markers mapped to the clone, distributors and fingerprint map information (see figure legends below for additional information on these tabs).


Figure 4a. Clone Record: Summary and Genome View Tab. The Genome View tab shows the selected clone placement in NCBI's Sequence Viewer in the context of known genes and other placed clones from the library to which it belongs. The clone of record is highlighted and shown at the top of the placement track. Use the pull-down menu to select the placement you want to view. Clicking on any placement will open a pop-up tooltip with details of the placement. For more information on NCBI's placement methodology, please see the placements FAQ page.

clone record summary


Figure 4b. Clone Record: Clone Placements Tab. This tab contains the details for all placements associated with the clone. This includes the identifiers of the assemblies on which it has been placed, the sequence coordinates and the placement concordancy and confidence (which indicates the degree of support for a given placement). Mousing over the data in the "Confidence" column will bring up a tooltip providing a definition for the specific value, while clicking on the data will take you to a legend describing all possible confidence values. Clicking the icon next to the table header will take you to a placements FAQ page that provides additional information regarding the placement methodology used by NCBI.

clone record placements


Figure 4c. Clone Record: Associated Sequences Tab. This tab provides the sequence identifiers and related information for all sequences associated with the clone. Clicking on any of these identifiers will take you to the sequence records in GenBank or the Trace Archives. Details for the data in "Category" column are available in pop-up tool tips or by clicking on the item.

clone record sequences

Figure 4d. Clone Record: Fingerprint Info Tab. For any clone that was fingerprinted at BCGSC, this tab provides the name of the fingerprint contig, number of bands and clone fingerprinting details. Fingerprinting data can be downloaded from BCGSC.

clone record fingerprint

Figure 4e. Clone Record: Clone Markers Tab. For genomic clones, this tab provides a listing of any markers that have been experimentally mapped to the clone. Clicking on an STS id will take you to the corresponding NCBI Probe DB record for that marker.

clone record marker

Figure 4f. Genomic Clone Record: Distributors Tab. For genomic clones, this tab provides a listing of the clone library distributors, as well as a link to the Clone DB distributors page.

clone record genomic dists

Figure 4g. Cell-based Clone Record: Distributors Tab. For cell-based clones, this tab provides information about the various formats in which the clone is distributed by the International Mouse Strain Resource (IMSR). Clicking the links in the table of this tab will take you to the corresponding search results page at IMSR.

clone record cell dists

Figure 4h. Cell-based Clone Record: Allele Info Tab. This tab provides the names of the alleles associated with cell-based (gene trap or gene targeting) clones. Links are provided to the corresponding allele and gene record pages at MGI, as well as the NCBI Entrez Gene record.

clone record allele info


5. Clone DB Entrez Search

A search bar is provided on the top of each Clone DB page with a drop-down menu to search Clone DB and other NCBI resources using Entrez (See Entrez Help for further details).
A Clone DB search returns clones, with links to their corresponding library and clone record pages. Library records are not included in Entrez search results, but if a search detects any libraries, users will find a prompt to the Clone DB library browers.

Advanced Search

/clone/advanced
The Clone DB Advanced search page allows the user to build up an Entrez search query choosing the search fields and values from drop-down menus.

Search Fields

The following search fields are available to search Clone DB:

Table 1: Clone DB Entrez Search Fields
Search Field Description
Accession [AcNum, ACC, ACCN, ACNUM] Accession of any internal or external identifier. Versions removed.
Accession Version [AccVer, ACCV, ACCVER] Accession and version of GENBANK accessions associated with clone records.
All Fields [ALL] Default
Alternate Library Abbreviation [AltLibAbbr, ALAB, ALTLIBRARY_ABBR, ALT_LIB_ABBR] Alternate Library Abbreviation
Alternate Library Name [AltLibName, ALN, ALTLIBRARY, ALT_LIB_NAME] Alternate Library Name
Assembly Accession [AssemAcc, ASSA] Accession of assembly on which placed
Assembly Name [AssemName, ASSN] Assembly on which placed
Breed [Breed, BREE] Breed
Cell Line [CellLine, CELL] Cell Line
Cell Type [CellType, CELT] Cell Type
Chromosome Accession [ChromAcc, CHRA, CHRACC, CHROM_ACC] Accession of chromosome on which placed
Chromosome Start [ChromStart, CHRB, CHRBEG, CHRSTART, CHROM_START] Chromosome start of placement
Chromosome Stop [ChromStop, CHRE, CHREND, CHRSTOP, CHROM_STOP] Chromosome end of placement
Clone Name [ClName, CLN, CLONE, CLONE_NAME] Clone Name
Clone Name Alias [ClAlias, CLA, CLONE_ALIAS] Clone Name Alias
Cultivar [Cultivar, CULT] Cultivar
Cultivar Accession [CultivarAcc, CUAC] Cultivar Accession provided in library submission XML
Development Stage [DevelStage, DEST] Development Stage provided in library submission XML
Gene Name [GeneName, GENE, GENE_NAME, SYM] Name or alias of Gene at same location as the placement of the clone
Gene ID [GeneID, GNID, ENTREZGENE_ID] GeneID of gene at same location as the placement of the clone
Gene Description [GeneDesc, GDSC, GENED, GENEFN, GENE_DESC, GENE_FULL] Full name (description) of gene at same location as the placement of the clone
GI [Gi, GI] GIs associated with clone records
Isolate [Isolate, ISOL] Isolate provided in library submission XML
Library Abbreviation [LibAbbr, LBR, LIB_ABBR, LIBRARY_ABBR] Library Abbreviation
Distributor [Distributor, DIST] Library Distributor Name, provided in library submission XML
Library Name [LibName, LIB, LIBN, LIBRARY] Library Name
Library Type [LibType, LIBT, LIBRARY_TYPE] Library Type
Object type [ObjType, OT, OBJ_TYPE] Object type in Clone DB (library, clone)
Organ [Organ, ORGA] Organ provided in library submission XML
Organism [Organism, ORG, ORGN] Organism name (exploded)
Placement Method [PlaceMethod, PLMT, PLACE_METHOD] Placement Method
Placement Confidence [PlaceConf, PLCN, PLACE_CONF] Placement Confidence
Population [Population, POPU] Population provided in library submission XML
Property [PROPERTIES] Clone properties. Possible values are: "Has Fingerprint", "Has End", "Has Insert", "Concordant" and "Placed"
Genome Project Id [PrjId, PID] Genome Project Id provided in library submission XML
PubMed ID [PMID, PUBMEDID] PubMed ID provided in library submission XML
Scaffold Accession [ScafAcc, SCFA] Accession of scaffold on which on which placed
Scaffold Start [ScafStart, SCFB, SCAF_START, SCAF_BEG] Scaffold start of placement
Scaffold Stop [ScafStop, SCFE, SCAF_STOP, SCAF_END] Scaffold stop of placement
Strain [Strain, STRA] Strain
STS [STS] STS's that have been mapped to any sequences associated with clone records
Taxonomy ID [TaxId, TXID, TAX_ID, TAXONOMY_ID, TAXONOMY] Taxonomy ID
TI [Ti, TI] TIs associated with clone records
Tissue [Tissue, TISS] Tissue provided in library submission XML
Vector [VectName, VN, VECT, VECTOR, VECT_NAME] Vector name provided in library submission XML
Vector Type [VectType, VT, VTYPE] Vector type provided in library submission XML
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Last updated: 2014-04-21T16:43:09-04:00