**1. Where do I start at NCBI ?**

NCBI provides a queryable interface that enables navigation between
inter-connected data types and between information for multiple genomes.
NCBI brings together the power of large-scale computational analyses and
an integrated system of data retrieval with detailed information on
maps, sequence, expression, genomes, genes, diseases, phenotypes,
publications, protein domains and structures. NCBI provides connections
between these disparate types of data by pre-computing related records.

Searches at NCBI can begin in many places. Among these are NCBI's home
page (<http://www.ncbi.nlm.nih.gov/> ), the Entrez home page
(<http://www.ncbi.nlm.nih.gov/Entrez>/), the Zebrafish Genome Resources
page (<http://www.ncbi.nlm.nih.gov/genome/guide/zebrafish>) and the
*Danio rerio* Taxonomy database home page
(<http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=7955&lvl=3&srchmode=1>
).

**1. NCBI's home page**

Explore links provided at NCBI's home page to navigate to NCBI's
databases, tools and resources. On NCBI's home page, links are provided
in the top menu bar, in the left blue bar and under the "Hot Spots"
header on the right. From the NCBI home page, submit a direct query
against any of the databases included in the pull down menu, including a
query against all **Entrez databases**.

Announcements of new and updated resources are provided on the NCBI home
page as Highlights in the center of the page and in detail in NCBI's
quarterly newsletter. NCBI's newsletter also includes additional
announcements, NCBI project descriptions and recent NCBI publications.

![](media/image1.png){width="4.927083333333333in"
height="6.145833333333333in"}

**2. Entrez home page**

The Entrez home page lists and provides links to all Entrez databases.
From the home page, all Entrez databases can be searched simultaneously
with a single query. Both simple (single text term) and more complex
queries are supported. Complex queries of one or more terms that include
boolean operators (AND, OR, NOT) and searches of specified fields. Field
qualifiers can be upper or lower case, for example: \[organism\],
\[ORGN\], \[taxonomy_id\], \[keyword\], or \[KYWD\]. A list of Entrez
Search Fields and Qualifiers for each Entrez database is also available
at:
(<http://www.ncbi.nlm.nih.gov/entrez/query/static/help/Summary_Matrices.html#Search_Fields_and_Qualifiers>).

![](media/image2.png){width="7.18125in" height="4.024305555555555in"}

**3. NCBI's Zebrafish Genome Resources**

Links to genome-specific resource pages can be found on the Genomic
Biology page (<http://www.ncbi.nlm.nih.gov/Genomes/index.html>). A link
to the Genomic Biology page is located in the left-hand blue side bar of
NCBI's home page.

The Zebrafish Genome Resources page
(<http://www.ncbi.nlm.nih.gov/genome/guide/zebrafish/index.html>)

was created to provide a gateway to web resources and includes links to
a number of NCBI sites and to external resources that may be of interest
to members of the zebrafish community. The Zebrafish Genome Resources
page also includes links to pre-set Entrez queries, including: papers or
sequences submitted to NCBI's PubMed or GenBank databases in the last 30
days or the current set of Zebrafish Gene Collection (ZGC) full-length
cDNA clones in GenBank.

![](media/image3.png){width="5.348611111111111in" height="4.0625in"}

**4. *Danio rerio* Taxonomy Page**

Entrez's Taxonomy page for *Danio rerio*
(<http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=7955&lvl=3&srchmode=1>)
provides another entry point to zebrafish data at NCBI. From the
Taxonomy home page
(<http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=taxonomy>), choose
the *Danio rerio* (zebrafish) link to view the *Danio rerio* Taxonomy
page. This page includes a table reporting the current number of
zebrafish entries in each Entrez database. The number of entries is
linked to the individual databases. Additionally, the *Danio rerio*
Taxonomy page includes the list of centers submitting Trace Archive
records. (Trace Archive:
<http://www.ncbi.nlm.nih.gov/Traces/trace.cgi>?) For each type of
**Trace Archive** record (Clone end, EST, Finishing, Shotgun, WGS, and
ALL), view the number of records and follow links, by type, to the Trace
Archive. The *Danio rerio* Taxonomy page also includes a list of links
to external resources **(LinkOuts**).

![](media/image4.png){width="6.875in" height="4.277777777777778in"}

**5. NCBI's FTP resources**

In addition to NCBI's web resources, NCBI also provides unrestricted
access to NCBI's software and genome data. **NCBI's FTP home page**:
(<http://www.ncbi.nlm.nih.gov/Ftp/index.html>) or directly from NCBI's
ftp: [ftp.ncbi.nih.gov](ftp://ftp.ncbi.nih.gov/).

**6. NCBI's Site Search**

A site search
(<http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=ncbisearch>) of NCBI
can be conducted either at NCBI's home page by selecting 'NCBI Web Site'
from the pull down menu in the top search bar found on most NCBI web
pages. Queries submitted from the Entrez home page includes a search of
NCBI's web pages.

**2. How do I find my gene ?**

1.  **How do I find my gene by searches based on text, sequence or map**

> **position ?**

Text searches submitted to the **Entrez Gene** database
(<http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene>) can include
any gene attribute including: symbol, name, alias, identifier (e.g. ZFIN
id, GeneID), accession, publication (PubMed ID), GO terms, linkage group
or chromosome.

![](media/image5.png){width="6.58125in" height="4.145833333333333in"}

Search for a gene of interest by submitting a BLAST search by choosing
the type of search from the **BLAST home page**
(<http://www.ncbi.nlm.nih.gov/BLAST>).

![](media/image6.png){width="6.1819444444444445in"
height="3.845833333333333in"}

BLAST tools enable searches against nucleotide or protein databases,
translational searches (protein vs. nucleotide), **MegaBLAST**
comparisons, genome specific BLAST pages (including a **zebrafish BLAST
page**: <http://www.ncbi.nlm.nih.gov/genome/seq/DrBlast.html>) and
BLASTing of two nucleotide or protein sequences via bl2seq.

![](media/image7.png){width="6.875in" height="4.5in"}

The "Options for advanced blasting" section on the BLAST query page
allows searches for hits against two organisms with the "AND" option or
to search for hits in either organism with the "OR" option such as:
*Xenopus tropicalis* OR *Takifugu rubripes*.

Alternatively, view the pre-computed nucleotide and protein sequence
comparisons available in NCBI's **HomoloGene**

( <http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=homologene>) and
BLink (e.g.<http://www.ncbi.nlm.nih.gov/sutils/blink.cgi?pid=42542497>)
resources.

Identify a gene of interest by it's map position. Search by linkage
group or chromosome in **Entrez Gene** or query map data by starting at
NCBI's **Map Viewer** home page (<http://www.ncbi.nlm.nih.gov/mapview/>)
or the zebrafish genome view page
(<http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=7955> ).

![](media/image8.png){width="6.395833333333333in"
height="4.7034722222222225in"}

Search zebrafish map data at the Map Viewer home page by selecting an
organism from the Search drop down menu and entering a gene symbol,
accession or alias to the query bar at the top of the page. Other terms
may be used for searching, depending on the data associated with each
organism.

Following the link to any of the organism-specific genome view pages
(from the Map Viewer home page), submit a search in the top menu bar or
click on the "Advanced Search" button to further specify their query.
For zebrafish, the search can be refined by linkage group, marker type
(SNP or non-SNP) or

the map name.

Map data can also viewed by choosing any of the LG links in the "Jump to
the Genome" figure on the **Zebrafish Genome Resources** page
(<http://www.ncbi.nlm.nih.gov/genome/guide/zebrafish>). These links go
directly to each linkage group in the zebrafish Map Viewer.

**2. How do I find my gene when a text search does not work ?**

One approach is to take advantage of the higher level of annotation
available for other organisms to find a gene of interest. Although a
gene may not yet be identified in one organism, it may be in another.
Even though a gene of interest may not yet be identified, in zebrafish
for example, mRNA or protein sequences representing that gene may be
available either in the sequence databases (**Entrez Nucleotide** or
**Entrez Protein**) or in an **Entrez Gene** record for an
uncharacterized gene.

To begin, search Entrez Gene by the gene name or gene symbol of
interest. If there is a matching Entrez Gene record, follow the links to
related records provided in the Links pull-down menu to look for related
mRNAs or proteins representing the zebrafish gene.

Following links to **Homologene** to view other highly related mRNAs and
proteins.

![](media/image9.png){width="5.3875in" height="5.552083333333333in"}

Each Homologene record also includes related **UniGene** clusters.
Examine the sequences included in the UniGene cluster by following the
link to the UniGene database. If an Entrez Gene record is associated
with the UniGene cluster, a link to Gene will be provided in the UniGene
Links menu.

![](media/image10.png){width="5.5875in" height="4.958333333333333in"}

Alternatively, follow the Protein link to **Entrez Protein** to view
related proteins by following the **BLink (BLAST Link)** associated with
the Protein record. BLink provides a graphical display to view the
pre-computed protein comparisons between the query protein and all other
proteins in Entrez Protein. These results may identify a zebrafish
protein that is highly similar to the query protein. Check the Links
associated with the Entrez Protein record to determine if that protein
is associated with an Entrez Gene record.

![](media/image11.png){width="6.503472222222222in"
height="4.895833333333333in"}

3.  **How can I find the zebrafish homolog of a recently cloned mouse**

> **gene?**

If searches of the pre-computed comparisons in HomoloGene or BLink do
not yield any likely candidates, another approach would be to submit a
search of the mouse gene symbol to Entrez's home page to determine if a
similarly named zebrafish gene exists.

Alternatively, Homologene comparisons may have already identified a
UniGene cluster containing ESTs or uncharacterized cDNAs that represent
the zebrafish homolog. If a ZFIN marker or Entrez Gene record contains
these uncharacterized sequences, a link to ZFIN or Entrez Gene will be
at the top of the UniGene page.

**3. How do I find gene-related information ?**

**1. What gene-related information is available in Entrez Gene ?**

![](media/image12.png){width="6.46875in" height="4.1715277777777775in"}

Entrez Gene records include gene symbols, gene names, links to external
data providers (e.g. ZFIN, MGI, HGNC), aliases, related sequences
(including RefSeqs (<http://www.ncbi.nlm.nih.gov/R0fSeq/>), map
location, taxonomy information and links to publications (PubMed),
marker information linked to **UniSTS**
(<http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unists>). Links to
other related resources are included at the bottom of the Entrez Gene
page and in the Links pull-down menu.

![](media/image13.png){width="6.291666666666667in"
height="4.430555555555555in"}

View suggested query options by clicking on the Limits tab at the top of
the Entrez Gene page
(<http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=Limits&DB=gene>).

Subscriptions to announcement lists for changes to the RefSeq, Entrez
Gene and Map Viewer projects are available. Links to the Subscription
information pages are found at the bottom of the blue side bar in Entrez
Gene.

**RefSeq announce**:
<http://www.ncbi.nlm.nih.gov/mailman/listinfo/refseq-announce>

**Gene announce**:
<http://www.ncbi.nlm.nih.gov/mailman/listinfo/gene-announce>

**Map Viewer announce**:
<http://www.ncbi.nlm.nih.gov/mailman/listinfo/mapview-announce>

**2. How do I identify a likely homolog for my gene ?**

Highly related nucleotide and protein sequences representing putative
homologs between multiple genomes are identified through computational
analysis and presented in the Homologene database.

Submit a text based query to HomoloGene from the Homologene home page,
(<http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=homologene>), the
Entrez home page or by choosing Homologene from any of the Search bars
found at the top of most NCBI pages.

Links to Homologene are also provided in the drop down Links menu of the
other Entrez databases including Entrez Gene, UniGene, Entrez
Nucleotide, Entrez Protein, Taxonomy, GEO and PubMed.

**3. Is my gene annotated on the zebrafish whole genome assembly ?**

As NCBI has done for projects, the zebrafish genome sequence will become
available in NCBI's Map Viewer when the zebrafish assembly sequences are
accessioned in GenBank/DDBJ/EMBL. At that time, the zebrafish genome
sequence will be added to the set of organisms included in NCBI's genome
pipeline.

**4. What map data is available for zebrafish at NCBI ?**

The Zebrafish Map Viewer
(<http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=7955> ) at NCBI
includes the LN54 and T51 radiation hybrid maps, the genetic maps (MGH,
HS, MOP, GAT), the Zebrafish Genome Integrated Map (ZMAP), and the SNP
(Single Nucleotide Polymorphism) variation map.

**5. What other genes, ESTs, STS markers or BACs are annotated near**

**my gene ?**

Search NCBI's **Map Viewer** to identify candidate genes or markers in a
region of interest. View marker placement on the genetic and radiation
hybrid maps by submitting a text query.

Identify a BAC clone that contains a marker or gene of interest or that
is located in a specific genomic region by submitting a search to NCBI's
Clone Finder
(<http://www.ncbi.nlm.nih.gov/genome/clone/clonefinder/CloneFinder.html>).
At this time, Clone Finder searches are limited to mouse.

**6. How can I identify BAC and PAC clones that would aid me in
mapping**

**genomic clones to chromosomes?**

Find all mapped PACs or BAC_ENDs in NCBI's Map Viewer by submitting a
search based on the naming schema for zebrafish PACs and BACs. Serach
PACs with busm1\* and BAC_ENDs with bz\*.

NCBI's clone registry of genomic clones
(<http://www.ncbi.nlm.nih.gov/genome//clone/>) can be queried to view
sequence, library, map, and distributor information. View library
information for each organism in the Library Browser
(<http://www.ncbi.nlm.nih.gov/genome//clone/clbrowse.cgi>) and links to
clone distributors on the Distributors page
(<http://www.ncbi.nlm.nih.gov/genome//clone/distributors.html>). Follow
the pre-computed links associated with the nucleotide accession found on
the Clone page to mine the data stored in other NCBI databases including
UniSTS, UniGene, Map Viewer (for example:
<http://www.ncbi.nlm.nih.gov/genome/clone/clname.cgi?stype=Id&list=1145501&TransHist=0>).

**7. How do I find all ZGC clones ?**

Download the list of full-length clones
([http://zgc.nci.nih.gov](http://zgc.nci.nih.gov/) ) by clicking on the
Full Text button to view the Full length clone list or FASTA sequences
(<ftp://ftp1.nci.nih.gov/pub/MGC/fasta/>) from the ZGC web site
(<http://zgc.nci.nih.gov/>).

Another option is to submit a search against the Entrez Nucleotide
database: "Danio rerio \[organism\] AND biomol_mrna \[properties\] AND
MGC \[keyword\]" (

[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&db=Nucleotide&orig_db=Nucleotide&Nucleotidefilters=truen&term=Danio+AND+rerio+AND+MGC\[KYWD](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&db=Nucleotide&orig_db=Nucleotide&Nucleotidefilters=truen&term=Danio+AND+rerio+AND+MGC[KYWD)\]).

A short-cut has also been provided for this query on the Zebrafish
Genome Reources page
(<http://www.ncbi.nlm.nih.gov/genome//guide/zebrafish/>).

**8. How do I find library information for a ZGC clone ?**

From the ZGC home page (<http://zgc.nci.nih.gov/>), choose the Table or
Full Text option in the ZGC Full-length Clone Information table to view
the zebrafish library list choose either the Table or Full text button
for the ZGC library list on the ZGC home page
(<http://zgc.nci.nih.gov/>) .

![](media/image14.png){width="5.979166666666667in" height="5.03125in"}

**9. Are there any SNPs associated with my gene?**

Query NCBI's Single Nucleotide Polymorphism (SNP) database

(<http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=snp>) (e.g. SNP
identifier, rs372494:
<http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=3729494> ).

Identify all zebrafish SNPs known to be associated with an Entrez Gene
record, by the submitting the query: snp_gene\[filter\] AND "Danio
rerio"\[organism\] to dbSNP.

Identify all mapped SNPs in NCBI's by submitting the query: zsnp\* to
the zebrafish genome view page.

![](media/image15.png){width="6.432638888888889in"
height="3.6770833333333335in"}

**10. What Entrez Gene records have links to the ZFIN's expression data
?**

Entrez Gene records contain links to the Gene Expression Database (GXD)
at ZFIN in the drop down 'Links' menu in the upper right corner of the
Entrez Gene page, for example:
<http://zfin.org/cgi-bin/webdriver?MIval=aa-xpatview.apg&OID=ZDB-XPAT-020319-2>.

Retrieve the list of all Entrez Generecords containing a GXD link with
the query: "Danio rerio"\[organism\] AND ZFIN\[Text Word\] AND
Expression\[Text Word\].

**11. What resources are available to find expression data ?**

Expression-related records in any of the Entrez databases can be found
by submitting a query from the Entrez home page

( <http://www.ncbi.nlm.nih.gov/Entrez/index.html>) (e.g. notochord AND
development AND \"Danio rerio\"\[organism\].

Additional expression-related resources include Gene Expression Omnibus
(GEO, <http://www.ncbi.nlm.nih.gov/geo/>) to view GEO datasets and
profiles. The GEO database can be queried by gene name, organism or
tissue, and provide an additional source of functional information for
multiple organisms**.** UniGene's DDD (Digital Differential Display, (
<http://www.ncbi.nlm.nih.gov/UniGene/info_ddd.html> ) provides gene
expression fingerprints for cancer cells and their normal counterparts
and UniGene's Library Browser
(<http://www.ncbi.nlm.nih.gov/UniGene/lbrowse2.cgi?TAXID=7955>) includes
the number of sequences and clusters associated with each library and
detailed library information.

**12. What are other possible ways to infer function for my gene?**

Entrez Gene records may include submissions to the Gene References into
Function (GeneRIF) database. GeneRIF submissions include short
descriptions of a gene's function and the associated publication.
Information on the GeneRIF project can be found at:
<http://www.ncbi.nlm.nih.gov/projects/GeneRIF/GeneRIFhelp.html>.

GeneRIFs can be submitted my the research community from any Entrez Gene
page by clicking on the Submit link found in the Bibliography gray bar
on the Entrez Gene details page (e.g.
<http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=30483>).

Conserved domains may also provide functional information. The Conserved
Domain database (CDD) can be queried by a text search (e.g. pham00757,
smart00261, cd00064 or Furin-like) from the Entrez home page
(<http://www.ncbi.nlm.nih.gov/gquery/gquery.fcgi>) or directly from the
CDD home page (<http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cdd>)
to domain details and an alignment of proteins containing that domain.

Conserved domains can be identified by submitting a protein sequence
(accession, Gi or Sequence in FASTA format) to CDD's CD-Search form
(<http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi>).

Functional information can also be inferred from homologous sequences
identified in NCBI's Homologene database
(<http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi>). Submitting the
query "Danio rerio"\[organism\] against the Homologene database
identifies all Homologene sets that contain a related zebrafish UniGene
cluster.

**13. How do I find cDNAs that have been derived from a specific
library?**

One approach would be to go to the Zebrafish Gene Collection home page
(<http://zgc.nci.nih.gov/>), under the heading "ZGC Full-length Clone
Information" select the "Table" or "Full Text" buttons to view the ZGC
library list details (Library, Tissue, Vector or number of Clones). From
the ZGC home page ([http://zgc.nci.nih.gov](http://zgc.nci.nih.gov/)),
navigate to the ZGC library list page, choose the library name to go to
the Library Info Page or the Clones link to view the list of IMAGE ids,
GenBank accessions, symbols and the GenBank definition that correspond
to each sequenced clone.

Another approach would be to begin in UniGene, navigate to the details
for each EST by clicking on the EST accession number to view the
Sequence Information page. View the Library Description, the Sequence
Submitters, the number of UniGene clusters containing members of the
library or the number of sequences in each cluster by clicking on the
linked Library ID. The list of cDNAs for each cluster can be seen by
then clicking on the UniGene cluster number.

Example: zebrafish shield stage whole embryo (dbEST Library ID.9774)

<http://www.ncbi.nlm.nih.gov/UniGene/library.cgi?ORG=Dr&LID=9774> .

**14. Where can I find a list of all Entrez records for *Danio rerio*
?**

NCBI's Taxonomy database includes an index of the records included in
all Entrez databases for each organism represented by at least one
sequence in either the Entrez Nucleotide or the Entrez Protein database.

From the Taxonomy home page
(<http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Taxonomy>)

navigate to the zebrafish-specific page
(<http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=7955&lvl=3&srchmode=1>)
by clicking on the Danio rerio (zebrafish) link.

The **Taxonomy database** page also includes links to each linkage group
in Map Viewer and a table of Trace (raw DNA single-pass reads) record
counts from each sequencing center, divided by the type of Trace (for
example: CLONEEND, EST, FINISHING, SHOTGUN, WGS or ALL).

Further down the Taxonomy database page links are provided to external
resources pertinent to that organism. These links are called LinkOuts.
Detailed information on creating LinkOuts at NCBI can be found on the
**LinkOut** home page (<http://www.ncbi.nlm.nih.gov/entrez/linkout/>).

Near the bottom of the Taxonomy database page, the "Show organism
modifiers" link provide additional links to subsets of nucleotide (blue
number) and protein (red number) sequences based on their strain names,
isolate name, or specimen-voucher name. For example, clicking on the
blue SJD link returns the set of nucleotide records sequenced from the
SJD strain
([http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide&cmd=Search&dopt=DocSum&term=txid7955\[orgn\]+AND+strain+SJD\[tw](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide&cmd=Search&dopt=DocSum&term=txid7955[orgn]+AND+strain+SJD[tw)\]).

4.  **Where can I ask questions or submit suggestions ?**

NCBI welcomes questions and suggestions.

A link to contact information is provided at the bottom of the blue side
bar on the NCBI home page
(<http://www.ncbi.nlm.nih.gov/About/glance/contact_info.html>).

Submit questions directly to NCBI's Help Desk at
<info@ncbi.nlm.nih.gov>.

Questions or suggestions for NCBI's RefSeq, Entrez Gene or OMIM
databases can also be submitted via the Corrections form
(<http://www.ncbi.nlm.nih.gov/RefSeq/update.cgi>). A link to this form
is provided in the blue side bar of the Entrez Gene pages.