1. www.ncbi.nlm.nih.gov Bunu databases’in icine koy lecture 5i de sonuna
National Center for Biotechnology
Information (NCBI)
Bunu databases’in icine koy lecture 5i de sonuna
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2. Fig. 2.5
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3. Fig. 2.5
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5. PubMed is… National Library of Medicine's search service
16 million citations in MEDLINE
links to participating online journals
PubMed tutorial (via “Education” on side bar)
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6. Entrez integrates… the scientific literature;
DNA and protein sequence databases;
3D protein structure data;
population study data sets;
assemblies of complete genomes
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7. Entrez is a search and retrieval system that integrates NCBI databases
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8. BLAST is… Basic Local Alignment Search Tool
NCBI's sequence similarity search tool
supports analysis of DNA and protein databases
100,000 searches per day
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9. OMIM is… Online Mendelian Inheritance in Man
catalog of human genes and genetic disorders
edited by Dr. Victor McKusick, others at JHU
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10. Cancer Chromosomes
Contains cytogenetic, clinical, and reference information from integrated information from the NCI Mitelman Database of Chromosome Aberrations in Cancer, the NCI Recurrent Aberrations in Cancer database, and the NCI/NCBI SKY/M-FISH & CGH Database.

11. CDD
Conserved Domain Database, a collection of sequence alignments and profiles representing protein domains conserved in molecular evolution. Select 'Domains' from the Entrez pull down menu.

12. CoreNucleotide Contains all nucleotide sequences not included in the EST or GSS subsets.
3D Domains Contains protein domains from the Entrez Structure database.
EST A Nucleotide database subset that contains only Expressed Sequence Tag records.
Gene Genes and associated information for a number of organisms in addition to and including human.

13. Genome Genomes of over 1,200 organisms can be found in this database, representing both completely sequenced organisms and those for which sequencing is in progress.
Genome Project A searchable collection of complete and incomplete (in-progress) large-scale sequencing, assembly, annotation, and mapping projects for cellular organisms.
dbGaP Associated genotype and phenotype data.
GENSAT Gene expression atlas of the mouse central nervous system.

14. GEO Datasets Curated gene expression and molecular abundance DataSets from NCBI's Gene Expression Omnibus, a gene expression and hybridization array repository.
GEO Profiles Individual gene expression and molecular abundance profiles assembled from the GEO repository.

15. Books is…
searchable resource of on-line books
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16. TaxBrowser is… browser for the major divisions of living organisms
(archaea, bacteria, eukaryota, viruses)
taxonomy information such as genetic codes
molecular data on extinct organisms
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17. Structure site includes…
Molecular Modelling Database (MMDB)
biopolymer structures obtained from
the Protein Data Bank (PDB)
Cn3D (a 3D-structure viewer)
vector alignment search tool (VAST)
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18. Accessing information on molecular sequences
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19. Accession numbers are labels for sequences
NCBI includes databases (such as GenBank) that contain information on DNA, RNA, or protein sequences.
You may want to acquire information beginning with a
query such as the name of a protein of interest, or the
raw nucleotides comprising a DNA sequence of interest.
DNA sequences and other molecular data are tagged with accession numbers that are used to identify a sequence
or other record relevant to molecular data.
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20. What is an accession number?
An accession number is label that used to identify a sequence. It is a string of letters and/or numbers that corresponds to a molecular sequence.
Examples (all for retinol-binding protein, RBP4):
X GenBank genomic DNA sequence
NT_ Genomic contig
Rs dbSNP (single nucleotide polymorphism)
N An expressed sequence tag (1 of 170)
NM_ RefSeq DNA sequence (from a transcript)
NP_ RefSeq protein
AAC02945 GenBank protein
Q SwissProt protein
1KT7 Protein Data Bank structure record
DNA
RNA
protein
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21. Four ways to access DNA and
protein sequences
[1] Entrez Gene with RefSeq
[2] UniGene
[3] European Bioinformatics Institute (EBI)
and Ensembl (separate from NCBI)
[4] ExPASy Sequence Retrieval System
(separate from NCBI)
Note: LocusLink at NCBI was recently retired.
The third printing of the book has updated
these sections (pages 27-31).
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22. 4 ways to access protein and DNA sequences
[1] Entrez Gene with RefSeq
Entrez Gene is a great starting point: it collects
key information on each gene/protein from
major databases. It covers all major organisms.
RefSeq provides a curated, optimal accession number for each DNA (NM_006744)
or protein (NP_007635)
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23. From the NCBI home page, type “rbp4” and hit “Go” revised Fig. 2.7

24. revised
Fig. 2.7
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27. By applying limits, there are now just two entries

28. Entrez Gene (top of page)
Note that links to
many other RBP4
database entries
are available
revised
Fig. 2.8
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29. Entrez Gene (middle of page)

30. Entrez Gene (bottom of page)

31. Fig. 2.9
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32. Fig. 2.9
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33. Fig. 2.9
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34. FASTA format
Fig. 2.10
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35. What is an accession number?
An accession number is label that used to identify a sequence. It is a string of letters and/or numbers that corresponds to a molecular sequence.
Examples (all for retinol-binding protein, RBP4):
X GenBank genomic DNA sequence
NT_ Genomic contig
Rs dbSNP (single nucleotide polymorphism)
N An expressed sequence tag (1 of 170)
NM_ RefSeq DNA sequence (from a transcript)
NP_ RefSeq protein
AAC02945 GenBank protein
Q SwissProt protein
1KT7 Protein Data Bank structure record
DNA
RNA
protein
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36. NCBI’s important RefSeq project: best representative sequences
RefSeq (accessible via the main page of NCBI)
provides an expertly curated accession number that
corresponds to the most stable, agreed-upon “reference”
version of a sequence.
RefSeq identifiers include the following formats:
Complete genome NC_######
Complete chromosome NC_######
Genomic contig NT_######
mRNA (DNA format) NM_###### e.g. NM_006744
Protein NP_###### e.g. NP_006735
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37. NCBI’s RefSeq project: accession for genomic, mRNA, protein sequences
Accession Molecule Method Note
AC_ Genomic Mixed Alternate complete genomic
AP_ Protein Mixed Protein products; alternate
NC_ Genomic Mixed Complete genomic molecules
NG_ Genomic Mixed Incomplete genomic regions
NM_ mRNA Mixed Transcript products; mRNA
NM_ mRNA Mixed Transcript products; 9-digit
NP_ Protein Mixed Protein products;
NP_ Protein Curation Protein products; 9-digit
NR_ RNA Mixed Non-coding transcripts
NT_ Genomic Automated Genomic assemblies
NW_ Genomic Automated Genomic assemblies
NZ_ABCD Genomic Automated Whole genome shotgun data
XM_ mRNA Automated Transcript products
XP_ Protein Automated Protein products
XR_ RNA Automated Transcript products
YP_ Protein Auto. & Curated Protein products
ZP_ Protein Automated Protein products

38. Four ways to access DNA and
protein sequences
[1] Entrez Gene with RefSeq
[2] UniGene
[3] European Bioinformatics Institute (EBI)
and Ensembl (separate from NCBI)
[4] ExPASy Sequence Retrieval System
(separate from NCBI)
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39. DNA
RNA
protein
complementary DNA
(cDNA)
UniGene
Fig. 2.3
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40. UniGene: unique genes via ESTs
• Find UniGene at NCBI:
UniGene clusters contain many expressed sequence
tags (ESTs), which are DNA sequences (typically
500 base pairs in length) corresponding to the mRNA
from an expressed gene. ESTs are sequenced from a
complementary DNA (cDNA) library.
• UniGene data come from many cDNA libraries.
Thus, when you look up a gene in UniGene
you get information on its abundance
and its regional distribution.
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41. Cluster sizes in UniGene
This is a gene with
1 EST associated;
the cluster size is 1
Fig. 2.3
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42. Cluster sizes in UniGene
This is a gene with
10 ESTs associated;
the cluster size is 10

43. Cluster sizes in UniGene (human)
Cluster size (ESTs) Number of clusters
1  42,800
2 6,500
,500
,400
,100
,300
 ,128 
 ,000 21
16,000-30,000 8
UniGene build 194, 8/06

44. UniGene: unique genes via ESTs
Conclusion: UniGene is a useful tool to look up
information about expressed genes. UniGene
displays information about the abundance of a
transcript (expressed gene), as well as its regional
distribution of expression (e.g. brain vs. liver).
We will discuss UniGene further later
(gene expression).
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45. Five ways to access DNA and
protein sequences
[1] Entrez Gene with RefSeq
[2] UniGene
[3] European Bioinformatics Institute (EBI)
and Ensembl (separate from NCBI)
[4] ExPASy Sequence Retrieval System
(separate from NCBI)
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46. Ensembl to access protein and DNA sequences
Try Ensembl at for a premier
human genome web browser.
We will encounter Ensembl as we study the human genome,
BLAST, and other topics.

47. click
human

48. enter
RBP4

50. Five ways to access DNA and
protein sequences
[1] Entrez Gene with RefSeq
[2] UniGene
[3] European Bioinformatics Institute (EBI)
and Ensembl (separate from NCBI)
[4] ExPASy Sequence Retrieval System
(separate from NCBI)
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51. ExPASy to access protein and DNA sequences
ExPASy sequence retrieval system
(ExPASy = Expert Protein Analysis System)
Visit
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52. Fig. 2.11
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54. Example of how to access sequence data:
HIV-1 pol
There are many possible approaches. Begin at the main
page of NCBI, and type an Entrez query: hiv-1 pol
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56. Following the “genome” link yields a manageable three results
Searching for HIV-1 pol:
Following the “genome” link yields
a manageable three results
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57. Example of how to access sequence data:
HIV-1 pol
For the Entrez query: hiv-1 pol
there are about 40,000 nucleotide or protein records
(and >100,000 records for a search for “hiv-1”),
but these can easily be reduced in two easy steps:
--specify the organism, e.g. hiv-1[organism]
--limit the output to RefSeq!
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58. over 100,000
nucleotide entries
for HIV-1
only 1 RefSeq

59. Examples of how to access sequence data:
histone
query for “histone” # results
protein records
RefSeq entries
RefSeq (limit to human) 1108
NOT deacetylase 697
At this point, select a reasonable candidate (e.g.
histone 2, H4) and follow its link to Entrez Gene.
There, you can confirm you have the right gene/protein.

61. Access to Biomedical Literature
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62. PubMed at NCBI
to find literature
information

63. PubMed is the NCBI gateway to MEDLINE.
MEDLINE contains bibliographic citations
and author abstracts from over 4,600 journals
published in the United States and in 70 foreign
countries.
It has >14 million records dating back to 1966.
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64. MeSH is the acronym for "Medical Subject Headings."
MeSH is the list of the vocabulary terms used
for subject analysis of biomedical literature at NLM.
MeSH vocabulary is used for indexing journal articles
for MEDLINE.
The MeSH controlled vocabulary imposes uniformity
and consistency to the indexing of biomedical literature.
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67. PubMed search strategies
Try the tutorial (“education” on the left sidebar)
Use boolean queries (capitalize AND, OR, NOT)
lipocalin AND disease
Try using “limits”
Try “Links” to find Entrez information and external resources
Obtain articles on-line via Welch Medical Library
(and download pdf files):
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68. 1 AND 2 1 2
lipocalin AND disease
(60 results)
1 OR 2 1 2
lipocalin OR disease
(1,650,000 results)
1 NOT 2 1 2
lipocalin NOT disease
(530 results)
Fig. 2.12
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8/04

69. “globin” is present “globin” is absent
Article contents:
“globin” is
present
“globin” is
absent
Search result:
false positive
(article does not
discuss globins)
“globin” is
found
true positive
false negative
(article discusses
globins)
“globin” is
not found
true negative
8/06

70. WelchWeb is available at http://www.welch.jhu.edu

71. Brian Brown (bbrown20@jhmi.edu) and
Brian Brown and
Carrie Iwema are the
Welch Medical Library liasons to the basic sciences