1. NCBI Molecular Biology Resources

2. The International Sequence Database Collaboration
NIH
SRS
getentry
Entrez
Submissions
Updates
Sequin
BankIt
WebIn
SAKURA
NCBI
GenBank
EMBL
DDBJ
EBI
CIB
NIG
EMBL

3. Primary vs. Derivative DatabasesC GA
ATT GA C GA C
ATT GA
UniGene C
Algorithms
TATAGCCG
Sequencing
Centers
ACGTGC
ATTGACTA
ACGTGC
CGTGA
TTGACA
UniSTS
EST
GenBank
Updated
continually
by NCBI
STS
Updated ONLY
by submitters
RefSeq:
Annotation
Pipeline
GSS
HTG
INV
VRT
PHG
VRL
PRI
ROD
PLN
MAM
BCT
ACGTGC
RefSeq:
LocusLink and
Genomes Pipelines
Curators
TATAGCCG
AGCTCCGATA
CCGATGACAA
Labs

4. Types of Databases Primary Databases Derivative Databases
Original submissions by experimentalists
Remember biologyʼs Central Dogma: DNA → RNA → protein.
Primary refers to one dimensional ʻsymbolʼ information written in sequential order necessary to specify a particular biological molecular entity, be it polypeptide or polynucleotide.
Content controlled by the submitter
Examples: GenBank, SNP, GEO, PubChem Substance
Derivative Databases
Built from primary data
Content controlled by third party (NCBI)
Examples: Refseq, TPA, RefSNP, UniGene, Protein, Structure, Conserved Domain, PubChem Compound
Primary databases serve as a repository of experimentalist sequences (GenBank).
Derivative databases are sources of edited/curated sequences (RefSeq…reference sequences, UniGene...genes compared to genetic loci on genomes)

5. What is Entrez?
Entrez Global Query is an integrated search and retrieval system for databases of National Center for Biotechnology Information (NCBI).
It provides access to all NCBI databases simultaneously with a single query string and user interface.
Support boolean operators and search term tags to limit parts of the search statement to particular fields.
This returns a unified results page, that shows the number of hits for the search in each of the databases, which are also links to actual search results for that particular database.
A text search / retrieval engine NOT A DATABASE.
A tool for finding biologically linked data.
A virtual workspace for manipulating large datasets.

6. Entrez Databases Each record is assigned a UID
unique integer identifier for internal tracking
GI number for Nucleotide
Each record is given a Document Summary
a summary of the record’s content (DocSum)
Each record is assigned links to biologically related UIDs
Each record is indexed by data fields
[author], [title], [organism], and many others

7. The Entrez System Entrez Journals UniGene Books SNP PubMed UniSTS
Central
UniSTS
Nucleotide
PopSet
Protein
Entrez
ProbeSet
DNA/RNA overview
Genome
Structure
Taxonomy
CDD
3D Domains
OMIM

8. The Entrez System: Text Searches

9. Entrez Taxonomy
The backbone of NCBI
[organism]

10. An Entrez Database - Nucleotide
GenBank: Primary Data (97.9%)
original submissions by experimentalists
submitters retain editorial control of records
archival in nature
RefSeq: Derivative Data (2.1%)
curated by NCBI staff
NCBI retains editorial control of records
record content is updated continually

11. What is GenBank? NCBI’s Primary Sequence Database
Nucleotide only sequence database
Archival in nature
Each record is assigned a stable accession number
GenBank Data
Direct submissions (traditional records )
Batch submissions (EST, GSS, STS)
ftp accounts (genome data)
Three collaborating databases
GenBank
DNA Database of Japan (DDBJ)
European Molecular Biology Laboratory (EMBL) Database

12. A Traditional GenBank Record
LOCUS AY bp mRNA linear PLN 04-MAY-2004
DEFINITION Malus x domestica (E,E)-alpha-farnesene synthase (AFS1) mRNA,
complete cds.
ACCESSION AY182241
VERSION AY GI:
KEYWORDS .
SOURCE Malus x domestica (cultivated apple)
ORGANISM Malus x domestica
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots;
rosids; eurosids I; Rosales; Rosaceae; Maloideae; Malus.
REFERENCE 1 (bases 1 to 1931)
AUTHORS Pechous,S.W. and Whitaker,B.D.
TITLE Cloning and functional expression of an (E,E)-alpha-farnesene
synthase cDNA from peel tissue of apple fruit
JOURNAL Planta 219, (2004)
REFERENCE 2 (bases 1 to 1931)
TITLE Direct Submission
JOURNAL Submitted (18-NOV-2002) PSI-Produce Quality and Safety Lab,
USDA-ARS, Baltimore Ave. Bldg. 002, Rm. 205, Beltsville, MD
20705, USA
REFERENCE 3 (bases 1 to 1931)
JOURNAL Submitted (25-JUN-2003) PSI-Produce Quality and Safety Lab,
REMARK Sequence update by submitter
COMMENT On Jun 26, 2003 this sequence version replaced gi:
FEATURES Location/Qualifiers
source
/organism="Malus x domestica"
/mol_type="mRNA"
/cultivar="'Law Rome'"
/db_xref="taxon:3750"
/tissue_type="peel"
gene
/gene="AFS1"
CDS
/note="terpene synthase"
/codon_start=1
/product="(E,E)-alpha-farnesene synthase"
/protein_id="AAO "
/db_xref="GI: "
/translation="MEFRVHLQADNEQKIFQNQMKPEPEASYLINQRRSANYKPNIWK
NDFLDQSLISKYDGDEYRKLSEKLIEEVKIYISAETMDLVAKLELIDSVRKLGLANLF
EKEIKEALDSIAAIESDNLGTRDDLYGTALHFKILRQHGYKVSQDIFGRFMDEKGTLE
NHHFAHLKGMLELFEASNLGFEGEDILDEAKASLTLALRDSGHICYPDSNLSRDVVHS
LELPSHRRVQWFDVKWQINAYEKDICRVNATLLELAKLNFNVVQAQLQKNLREASRWW
ANLGIADNLKFARDRLVECFACAVGVAFEPEHSSFRICLTKVINLVLIIDDVYDIYGS
EEELKHFTNAVDRWDSRETEQLPECMKMCFQVLYNTTCEIAREIEEENGWNQVLPQLT
KVWADFCKALLVEAEWYNKSHIPTLEEYLRNGCISSSVSVLLVHSFFSITHEGTKEMA
DFLHKNEDLLYNISLIVRLNNDLGTSAAEQERGDSPSSIVCYMREVNASEETARKNIK
GMIDNAWKKVNGKCFTTNQVPFLSSFMNNATNMARVAHSLYKDGDGFGDQEKGPRTHI
LSLLFQPLVN"
ORIGIN
1 ttcttgtatc ccaaacatct cgagcttctt gtacaccaaa ttaggtattc actatggaat
61 tcagagttca cttgcaagct gataatgagc agaaaatttt tcaaaaccag atgaaacccg
121 aacctgaagc ctcttacttg attaatcaaa gacggtctgc aaattacaag ccaaatattt
181 ggaagaacga tttcctagat caatctctta tcagcaaata cgatggagat gagtatcgga
241 agctgtctga gaagttaata gaagaagtta agatttatat atctgctgaa acaatggatt
1801 aataaatagc agcaaaagtt tgcggttcag ttcgtcatgg ataaattaat ctttacagtt
1861 tgtaacgttg ttgccaaaga ttatgaataa aaagttgtag tttgtcgttt aaaaaaaaaa
1921 aaaaaaaaaa a //
Header
The Flatfile Format
Feature Table
Sequence

13. An Example Record – M17755 Field Indexed Terms
Indexing for Nucleotide UID
Field Indexed Terms
[primary accession] M17755
[title] Homo sapiens thyroid peroxidase (TPO) mRNA…
[organism] Homo sapiens
[sequence length] 3060
[modification date] 1999/04/26
[properties] biomol mrna
gbdiv pri
srcdb genbank

14. M17755: Feature Table TPO [gene name] CDS position in bp thyroiditis
[text word]
thyroid peroxidase
[protein name]
protein
accession

15. Sequence: 99.99% Accurate The sequence itself is not indexed…
Use BLAST for that!

16. RefSeq: NCBI’s Derivative Sequence Database
RefSeq database is a collection of taxonomically diverse, non-redundant and richly annotated sequences representing naturally occurring molecules of DNA, RNA, and protein.
Non-redundant nucleotide and protein sequences from plasmids, organelles, viruses, archaea, bacteria, and eukaryotes.
Updated to reflect current sequence data and biology
Each RefSeq is constructed wholly from sequence data submitted to the International Nucleotide Sequence Database Collaboration (INSDC).
Similar to a review article, a RefSeq integrates information across multiple sources at a given time hence provides a foundation for uniting sequence data with genetic and functional information.
They are generated to provide reference standards for multiple purposes ranging from genome annotation to reporting locations of sequence variation in medical records.

17. The common Refseq accession prefix
Molecular type
NC_
Complete genomic molecule (chromosome; microbial or organelle genome)
NT_
Genomic contig
NM_
Curated mRNA
XM_
mRNA (Computed)
NP_
Curated Protein
XP_
Protein (Computed)
NR_
Curated RNA
XR_
RNA(Computed)

18. Entrez Gene and RefSeq
Gene
GenBank
RefSeq
Nucleotide
Entrez Gene is the central depository for information about a gene available at NCBI, and often provides links to sites beyond NCBI
Entrez Gene includes records for organisms that have NCBI Reference Sequences (RefSeqs)
Entrez Gene records contain RefSeq mRNAs, proteins, and genomic DNA (if known) for a gene locus, plus links to other Entrez databases

19. Entrez Gene: RefSeq Annotations

20. Beyond RefSeq If your organism does not have RefSeqs…
UniGene : gene-based clusters of cDNAs and ESTs
WGS sequences in Entrez Nucleotide (wgs[prop])
Trace Archive

21. What is UniGene? A gene-oriented view of sequence entries
MegaBlast based automated sequence clustering
Now informed by genome hits New!
Nonredundant set of gene oriented clusters
Each cluster a unique gene
Information on tissue types and map locations
Includes known genes and uncharacterized ESTs
Useful for gene discovery and selection of mapping reagents
Clusters of ESTs based on automatic similarity. Each cluster represents a gene.

22. Organisms in UniGene Top Ten 1. Human 2. Rice 3. Mouse 4. Cow 5. Wheat
6. Zebrafish
7. Pig
8. Chicken
9. Frog (X. laevis)
10. Frog (X. tropicalis)

23. Finding UniGene Clusters
by link
by Entrez search

24. UniGene Cluster for TPO

25. Entrez Protein GenPept (DDBJ, EMBL, GenBank) 4,444,405
RefSeq ,753,167
PIR ,395
Swiss Prot ,005
PDB ,621
PRF ,079
Third Party Annotation ,219
Total ,693,891
The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.

26. Protein Sources and Links
PIR
no mRNA!
RefSeq
 NM_000537
SWISS-PROT
no mRNA!
GenPept
 M17755

27. PubMed is the NCBI gateway to MEDLINE.
MEDLINE contains bibliographic citations and author abstracts from over 4,000 journals published world-wide. It has 12 million records dating back to 1966.
In order to impose uniformity and consistency to the indexing of biomedical literature MeSH vocabulary is used for indexing journal articles for MEDLINE.
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.

30. Taxonomy Browser is…
browser for the major divisions of living organisms
(archaea, bacteria, eukaryota, viruses)
taxonomy information such as genetic codes
molecular data on extinct organisms

31. 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)

32. OMIM is… Online Mendelian Inheritance in Man
catalog of human genes and genetic disorders
edited by Dr. Victor McKusick, others at JHU

35. General Protein Databases
SWISS-PROT
Manually curated
high-quality annotations, less data
GenPept/TREMBL
Translated coding sequences from GenBank/EMBL
Few annotations, more up to date
PIR
Phylogenetic-based annotations
All 3 now combining efforts to form UniProt (
Unlike the main nucleotide sequence databases which all contain the same sequence data, the main public protein sequence databases all have their different “personality”.
SWISS-PROT, which comes, not so surprisingly, from Switzerland, is a manually curated database. As such it has very high quality, consistent annotations, which make it very suitable to keyword searching. However, since the validation and annotation processes take time, SWISS-PROT does not contain as much data as other protein databases. SWISS-PROT has recently become private and as such is available freely only to academics.
GenPept and TrEMBL are databases generated automatically by translating coding sequences (CDS features) from Genbank and EMBL respectively. TrEMBL sequences eventually get annotated and transferred into SWISS-PROT. The quality of annotations in these databases is not as high as that of SWISS-PROT but these databases are a lot more up to date than SWISS-PROT
PIR is also annotated but its annotations are different from those of SWISS-PROT. The format is often less convenient for text searching but entries contain information about the record’s superfamily which is often hard to find in other databases.

36. Swissprot format

37. Non-redundant Databases
Sequence data only: cannot be browsed, can only be searched using a sequence
Combine sequences from more than one database
Examples:
NR Nucleic (genbank+EMBL+DDBJ+PDB DNA)
NR Protein (SWISS-PROT+TrEMBL+GenPept+PDB protein)
The existence of several sequence databases which may not necessarily contain the same sequence information can present a problem when attempting to search as many sequences as possible: either one searches every database and gets mostly the same entries repeated across the many databases (not to mention the extra work of repeating the same search with different databases) or one searches only a subset of available databases and risks missing out on some valuable entry.
This concern is now addressed by creating non-redundant databases which combine several databases together and remove the duplicate entries. So for example, the non-redundant nucleotide database maintained at NCBI contains Genbank plus the sequences in EMBL which are not in Genbank plus the sequences in DDBJ which are not Genbank or EMBL plus the sequences in PDB Nucleic which are not in any of the other 3 databases.
Non-redundant databases built from a collection of databases usually contain only sequence data since the annotation format is not consistent across databases. Note also that in the process of removing duplicate sequences, some very similar but not perfectly identical sequences (including variants, mutations etc) can be removed from the non-redundant database.

38. Protein domain databases
Pfam (
Collection of multiple sequence alignments and hidden Markov models covering many common protein domains and families
SMART (a Simple Modular Architecture Research Tool)
Identification and annotation of genetically mobile domains and the analysis of domain architectures (
CDD (
Combines SMART and Pfam databases
Easier and quicker search

39. Sequence Motif Databases
Scan Prosite ( and PRINTS (
Store conserved motifs occurring in nucleic acid or protein sequences
Motifs can be stored as consensus sequences, alignments, or using statistical representations such as residue frequency tables
A sequence motif is a pattern of conservation in a group of sequences which reflects a common function or structure in these sequences.
Motifs can be represented in several ways in a computer, and the type of analysis that can be performed with the motif depends on the representation.
For example, the most common representation for a motif is a consensus sequence which shows which residues are allowed or not allowed at each position of the sequence. This type of representation is very common in the literature but has a number of drawbacks in that it provides only a qualitative description of the motif. As a result consensus sequences are either too specific and do not represent all the motifs they are meant to be represent, or they are not specific enough and match false positives.
Other representations of motifs include multiple sequence alignments of the sequences, and numerical representations such as profiles and weight matrices which assign a “weight” to each possible residue in the motif. Hidden Markov models (HMMs) are statistical representations of motifs where each possible residue at each position is assigned a probability which can be dependent not only on the position but also on its neighborhood.