NCBI: Entrez Home

Practical lesson 2

The NCBI WWW server and Entrez, part 1.

Obtaining information about your favorite genes (in this case, bofC and csbX, from Bacillus subtilis)

Open Netscape or a similar browser and make a connection to the NCBI server, at the address: http://www.ncbi.nlm.nih.gov/
Open Entrez, the general interface to NCBI's databases.
Search the Nucleotide database with the expression Bacillus subtilis bofC.
You will see a list of entries that contain, in any field and in any order, those three terms.
Because it may give you a faster answer, select the entry that contains less genes (X93081).

A complete entry in GenBank format will be displayed. From the Header section you will learn that the source of the sequence contained in entry X93081 is Bacillus subtilis. From the Features section, you will learn that the sequence encodes four genes, two of which have bofC and csbX as names.

Select Send to text, to generate a plain text version of the entry, that you could save.

Select Display FASTA, to obtain the nucleotide sequence in FASTA format.
Select Display Graphics, to obtain a linear map and the sequence of entry X93081.

Selecting now Protein coding genes you will obtain the Protein Translation Table.

Search, in the Features section, the part were the second CDS is described. In addition of having the aminoacid translation of the CDS on this document, you can jump to the Protein database.

You will access the GenBank formatted entry of protein CAA63620.1.
By clicking on the link Blink you will gain access to information about proteins with a similar sequence to that in CAA63620.1: first, you will learn that bofC has been assigned to a certain family or group of proteins from the COG database; second, you will get a list proteins that have been identified as similar to BofC by performing a standard BLAST search.
By clicking on the link Domains, you will get information about the presence in BofC of conserved domains. In this case, the protein includes a conserved domain identified in the Pfam database, which is characteristic of sugar transporters.

By clicking on the graphical representation of the domain, you will get a multiple sequence alignment of the family members.
By clicking on Show Domain Relatives, you will get a graphical representation of proteins that include related domains.

Browsing the taxonomy database to retrieve molecular information about your favorite group of organisms (in this case, Viruses).

Open Netscape or a similar browser and make a connection to the NCBI server, at the address: http://www.ncbi.nlm.nih.gov/
Open Entrez, the general interface to NCBI's databases.
Select the Taxonomy database and then click on Tax Browser , or on the word "tree" that appears in the explanatory text of the upper part.

Select Protein y Structure (for example) and click on Display.
You will get information about how many protein sequence and protein structure entries exist in the NCBI databases, for each of the viral species included in the list. Both the entries with protein sequences and the entries with structural information can be accessed from here.

Taxonomic information about Arabidopsis.
A table with links to information about each of the Arabidopsis thaliana chromosomes.

By clicking on the chromosome identifiers you will access pages with chromosomal maps, and links to files foe all the genes and proteins from Arabidopsis.

A table that compiles links to entries in other NCBI databases, related with Arabidopsis.
Links to databases at other institutions, that also contain information about Arabidopsis.

Obtaining general and molecular information about your favorite genetic disease (in this case, alopecia).

Open Netscape or a similar browser and make a connection to the NCBI server, at the address: http://www.ncbi.nlm.nih.gov/
Open Entrez, the general interface to NCBI's databases.
Select the OMIM database.

You will find that there are more than 140 entries (that appear in groups of 20), that contain the term alopecia in their description.

Select Search Morbid Map, on the right side of the page. You will get a catalog of genetic diseases.

By clicking on the numeric identifier of the column labeled as Disorder , you will access a document with information about the disease, supported with bibliographic information.
In the column labeled as Location you will see information about the chromosomal location of mutations that have been associated with the disease: chromosome number 8, short arm (identified with the letter "p"; the long arm is represented with the letter "q"). The number "21.2" indicates the location in terms of the band, as detected by the Giemsa method.
By clicking on the numeric identifier of the column labeled as OMIM, you will access to a document with information about the locus or gene that has been identified as affected by the mutations that cause the disease, and links to other sources of information.

By clicking on LocusLink, on the left side, you will access to the main page of this locus in LocusLink.

By clicking on the numeric identifier of the locus (55806) you will access to the LocusLink entry, which contains:

A diagram (the red line and rectangles in the upper part) that shows the structure of the gene in terms of exons and introns. From this diagram you can access to information about evidences that support the proposed structure.
A collection of links to other databases with information about the locus (colored rectangles).
A summary with information about several aspects of the gene: tissue specific expression, annotations from GenRIF, classification according to the Gene Ontology, related entries in nucleotide and protein sequence databases, homologous genes, etc.

Among the databases that can be accessed from the LocusLink entry, you will find:

February 2004

Manuel J. Gómez
Grupo de Diseño de Proteínas
Centro Nacional de Biotecnología, CSIC