Transcript Will Entrez Find Every Sequence Record?

NCBI’s Bioinformatics
Resources
Michele R. Tennant, Ph.D., M.L.I.S.
Health Science Center Libraries
January 2016
Entrez
Nucleotides
Entrez Nucleotides (GenBank)
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Database of nucleotide sequences
(ATGC)
Actually contains data from several
databases - GenBank, EMBL, DDBJ,
RefSeq
Hard to search because many submitting
scientists send in redundant information
and poorly annotated information
Nucleotide Data Domain
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As of December 15, 2015
• Over 203,939,111,071 bases
• Over 189,232,925 sequence records
• Some complete genomes and chromosomes
So Why So Hard to Search?
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No controlled vocabulary - lose power of MeSH must OR synonyms. Often miss the records you
want.
Archival - quality of annotations depends on the
submitter (especially features field); little to no
quality control; spelling errors! Often miss the
records you want.
Redundant - lots of records for the same gene;
partial records, etc. Often pull up records you don’t
want.
GenBank Sample Record
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Before searching, we will look at a
GenBank sample record
Note that the “Features” field provides
useful biological information, and may
be searched
“Definition” field
acts as record title
– search [titl]
Click any link in
sample record to
access definition
of field and
search tips
Unique identifier; assigned
by NCBI; required by
journals/grants
Link to PubMed
citation/abstract
The “Features” field
provides the most
biological information;
search as [fkey]
Numbers
indicate location
on the
nucleotide
sequence
…3158
GenBank Identifiers
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Accession Number - U49845 [accn]
• Unique identifier; does not change
• Letter prefix no longer has significance
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Version - U49845.1
• If any change to sequence, version
U49845.2 created
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GenInfo Identifier (GI number) [uid]
• Run parallel to accession.version system;
change in sequence changes number
Searching “Nucleotides”
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Database is difficult to search:
• Redundant records
• Archival - poor or missing annotation
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Best searches are done using
commands; need a class to learn all
Practice search – search for sequences
for human presenilin 1
• Is there anything odd about the some of the
retrieved results?
Choose “nucleotide”
from dropdown, then
click “search”
Search for HUMAN
presenilin 1
But end up with
rat, mouse, etc.
Searching “Nucleotides”
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We retrieved the non-human and PSEN2
(rather than PSEN1) records because the
computer looked for the terms “human” and
“presenilin 1” ANYWHERE in the record (click
on details tab to see how the computer
parsed your search)
Use complex boolean searching to clean this
up: term [field] AND term [field]
Searching “Nucleotides”
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How to get rid of non-human sequences?
• Search human [orgn] (this works for any taxon)
How to get rid of non-presenilin 1 sequences?
• Another trick – search PSEN1 [gene]
• Note – you may miss relevant sequences, but should not pick up
irrelevant sequences
• The sequences that you miss are the ones that have not been
annotated with the current official gene symbol in the “gene” field
• DO NOT use this method if you need to find every sequence for a
particular gene
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Human [orgn] AND PSEN1 [gene]
This is the search that was
completed using fields
(orgn, gene) and filters
Use these filters to choose
molecule type, confine to
RefSeq records
How Can I Find “Best” Sequences
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Non-redundant, curated subset of the sequence data
domains
Contains one record for each gene or splice variant
from each organism represented
Records can be thought of as “review articles” for
sequences
“Best” (usually longest) sequence used as seed
Value-added annotations provided by experts
Easy – a tab now exists to limit retrieval to just
RefSeq
The typical RefSeq
accession number
format: 2 letters, an
underscore, and
then numbers
Click on the RefSeq link to retrieve
only the “best” sequences (highly
annotated, complete, nonredundant)
Viewing Formats
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The “Default” view is the standard
GenBank record
Researchers often use the “FASTA”
format for analysis
Change the record format at the
“Display” pull-down menu
Entrez
Proteins
Entrez Proteins
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Contains data from several databases:
• SwissProt, PIR, PRF, PDB
• Translations from annotated coding
regions in GenBank and RefSeq
Redundant archival data domain of
publicly available protein sequences
Searching Entrez Proteins
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Searched like Entrez Nucleotides
“Filters” choices differ; includes
molecular weight and sequence length
filters
Entrez Gene
Entrez Gene
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Pulls together information (sequences,
structures, literature, gene models,
pathways, etc.) for genes
Best place to start for “gene-centered” info
One record per gene per organism
Search by names, symbols, accessions,
publications, GO terms, chromosome
numbers, E.C. numbers, etc.
Search using
gene symbol
Could have searched
under any of these aliases
(unlike GenBank where
you would have to try
them all)
Official gene
symbol as
determined by the
Human Genome
Nomenclature
Commission
Summary of protein,
function and diseasecausing mutations;
from RefSeq record
Links to PubMed
records that
provide evidence
of function – any
researcher can
add these
Gene Ontology terms form a controlled
vocabulary with three components –
biological process, molecular function,
and cellular component
Links to OMIM
records of
phenotype/ disease
Links to protein
interactions
Links to
homology
maps
Pathway info may be
available from the
Kyoto Encyclopedia of
Genes and Genomes
Sequence and
domain links
Links to
GeneReviews
– clinical
resource
Taxonomy
Browser
Search Taxonomy Browser
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How many genera from the family
Iguanidae are represented by sequence
data?
How many nucleotide and protein
sequences are available for the family?
Entrez
Searching
Summary
To Find Everything(?)
Broaden Search
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OR together synonyms
OR together related terms (gene name, gene symbol,
protein name, alternate spellings, disorder)
Don’t specify a field- search entire record
Truncation - use * at end of word root
Click “Similar articles”
Try using Taxonomy Browser to pick up all taxa in a
particular group
Fewer/Best Records
Narrow Search
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Search particular fields:
• PubMed - MeSH Browser,
subheadings, major MeSH
• Nucleotide - features, title, gene,
properties, organism
Use “Filters”
Search only the RefSeq database
Will Entrez Find
Every Sequence Record?
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No!!!
• Entrez relies on annotation of records, so you are
searching solely on “terminology”
• Some records are not annotated, some records are
poorly or incorrectly annotated
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To find all useful sequences – need to search
on sequence itself
• BLAST
Entrez “Similar Articles”
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PubMed similar articles
• Based on a “word weight” algorithm – MeSH, title,
abstract words
• In order by weight (highest weight first)