Transcript PubMed and NCBI

LSM2241
P1 & P2 – Extra Discussion Questions
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Features of major databases
(PubMed and NCBI Protein Db)
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Anatomy of PubMed Db
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Epub ahead of print and journal
impact factor
How to get impact factor of any journal:
1) Direct source – web of science database (free for NUS students)
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2) In direct source, e.g blogs, sites etc (do Google search)
Anatomy of a PubMed record
Extra information compared to slide 3
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Demo on downloading articles
AccessingOnlineJournalArticles.ppt for details
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Anatomy of a Protein Db
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Accession numbers and GenInfo Identifiers
NM_000546.3
120407067
GI (or Geninfo Identifier)
Accession
Version
120407067
NM_000546
NM_000546.3
Popular data sources:
dbj – DDBJ (DNA Data Bank of Japan database)
emb – The European Molecular Biology
Laboratory (EMBL) database
prf – Protein Research Foundation database
sp – SwissProt
gb – GenBank
pir – Protein Information Resource
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Why do we need accession number and
GI for one record?
1) What is the difference between accession and GI?
2) Why do we need these two when both seem to be
accession numbers?
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Why do we need accession numbers and
GIs?
ACCESSION
NM_000546
NM_000546
Sequence_v1
Version
GI
NM_000546.1
4507636
VERSION
NM_000546.3
NM_000546.2
NM_000546.1
GI
120407067
8400737
4507636
NM_000546
NM_000546
Sequence
update
Sequence_v2
NM_000546.2
8400737
Sequence
update
Sequence_v3
NM_000546.3
120407067
Q1) Which revision will NCBI show if you were to search by
the accession only without the version number?
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Accession numbers
-The unique identifier for a sequence record.
-An accession number applies to the complete record.
- Accession numbers do not change, even if information in the record
is changed at the author's request.
-Sometimes, however, an original accession number might become
secondary to a newer accession number, if the authors make a new
submission that combines previous sequences, or if for some
reason a new submission supercedes an earlier record.
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GenInfo Identifiers
- GenInfo Identifier: sequence identification number
- If a sequence changes in any way, a new GI number will be assigned
- A separate GI number is also assigned to each protein translation
Within a nucleotide sequence record
-A new GI is assigned if the protein translation changes in any way
-GI sequence identifiers run parallel to the new accession.version
system of sequence identifiers
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Version
- A nucleotide sequence identification number that represents a single,
specific sequence in the GenBank database.
-If there is any change to the sequence data (even a single base), the
version number will be increased, e.g., U12345.1 → U12345.2, but
the accession portion will remain stable.
-The accession.version system of sequence identifiers runs parallel to
the GI number system, i.e., when any change is made to a sequence,
it receives a new GI number AND an increase to its version number.
-A Sequence Revision History tool
(http://www.ncbi.nlm.nih.gov/entrez/sutils/girevhist.cgi)
is available to track the various GI numbers, version numbers, and
update dates for sequences that appeared in a specific GenBank record
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Anatomy of a Protein Db record
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Fasta Sequence
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Fasta Format
• Text-based format for representing  nucleic acid
sequences or peptide sequences (single letter codes).
• Easy to manipulate and parse sequences to programs.
Description line/row
Sequence data line(s)
Description line/row
Sequence data line(s)
>SEQUENCE_1
MTEITAAMVKELRESTGAGMMDCKNALSETNGDFDKAVQLLREKGLGKAAKKADRLAAEG
LVSVKVSDDFTIAAMRPSYLSYEDLDMTFVENEYKALVAELEKENEERRRLKDPNKPEHK
IPQFASRKQLSDAILKEAEEKIKEELKAQGKPEKIWDNIIPGKMNSFIADNSQLDSKLTL
MGQFYVMDDKKTVEQVIAEKEKEFGGKIKIVEFICFEVGEGLEKKTEDFAAEVAAQL
>SEQUENCE_2
SATVSEINSETDFVAKNDQFIALTKDTTAHIQSNSLQSVEELHSSTINGVKFEEYLKSQI
ATIGENLVVRRFATLKAGANGVVNGYIHTNGRVGVVIAAACDSAEVASKSRDLLRQICMH
Fasta Format (cont.)
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Begins with a single-line description, followed by lines of sequence data.
Description line
– Distinguished from the sequence data by a greater-than (">") symbol.
– The word following the ">" symbol in the same row is the identifier of the sequence.
– There should be no space between the ">" and the first letter of the identifier.
– Keep the identifier short and clear ; Some old programs only accept identifiers of only 10
characters. For example: > gi|5524211|Human or >HumanP53
Sequence line(s)
– Ensure that the sequence data starts in the row following the description row (be careful of
word wrap feature)
– The sequence ends if another line starting with a ">" appears; this indicates the start of another
sequence.
Description line/row
Sequence data line(s)
Description line/row
Sequence data line(s)
>SEQUENCE_1
MTEITAAMVKELRESTGAGMMDCKNALSETNGDFDKAVQLLREKGLGKAAKKADRLAAEG
LVSVKVSDDFTIAAMRPSYLSYEDLDMTFVENEYKALVAELEKENEERRRLKDPNKPEHK
IPQFASRKQLSDAILKEAEEKIKEELKAQGKPEKIWDNIIPGKMNSFIADNSQLDSKLTL
MGQFYVMDDKKTVEQVIAEKEKEFGGKIKIVEFICFEVGEGLEKKTEDFAAEVAAQL
>SEQUENCE_2
SATVSEINSETDFVAKNDQFIALTKDTTAHIQSNSLQSVEELHSSTINGVKFEEYLKSQI
ATIGENLVVRRFATLKAGANGVVNGYIHTNGRVGVVIAAACDSAEVASKSRDLLRQICMH
Amino acids
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IUPAC One Letter Amino Acid Code
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•
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A
B
C
D
E
F
G
H
I
J
K
L
M
Alanine
ASx
Cysteine
Aspar(D)ic Acid
Glutamic Acid
(F)enylalanine
Glycine
Histidine
Isoleucine
Lysine
Leucine
Methionine
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•
•
•
•
•
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•
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N
O
P
Q
R
S
T
U
V
W
X
Y
Z
Asparagi(N)e
Aspartic Acid
22nd (Pyl) Pyrr(O)lysine
Asparagine
Proline
ASx
(Q)lutamine
Arginine
(R)ginine
Glutamic Acid
Serine
Glutamine
Threonine
GLx
21st (Sec)Selenocysteine Lysine
Valine
Phenylalanine
T(W)ptophan
Tyrosine
Tryptophan
T(Y)rosine
21st (Sec) Selenocysteine
GLx
22nd (Pyl) Pyrrolysine
Note
Amino acid
Three letter code
Single letter code
Asparagine or aspartic acid
Asx
B
Glutamine or glutamic acid,
GLx
Z
Leucine or Isoleucine,
Xle
J
Unspecified or unknown amino acid
Xaa
X
Advice
• We highly recommend that you memorize the
amino acid codes and their structures (covered in
lectures on 3D structures)
• Memorizing the codes and in particular the
structures will be very useful for this module and
other modules, especially for research purposes.
• It is not compulsory that you memorize these for
this module.
Features of major database
(Gene Db)
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Anatomy of Gene Db
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Anatomy of a Gene Db record
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A section of Gene Db record:
Reference Sequences
mRNA
Accession
number
Protein
Accession
number
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Questions
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A) Problem Scenario
Mr. Tan Yong Liang, Benjamin just joined Prof. Tan
Tin Wee’s lab to do his PhD. He is to continue the
project that was done by Dr. Asif M. Khan, who just
graduated from Prof. Tan’s lab with PhD. To better
understand the project that Dr. Khan did, Prof. Tan
asked Benjamin to read all the papers that were
published by him. Benjamin being a newbie to
bioinformatics, needs your help in finding the papers.
Can you help him answer the following questions?
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A) Questions
Q1. Which database(s) should he search?
Q2. Help him formulate his search query based on the following available
information:
1.
2.
3.
Corresponding authors: Vladimir Brusic, Thomas J August, Tan Tin Wee
In one of the paper, Dr. Asif M. Khan’s name was incomplete: Asif Khan
Prof. August has a paper with Rosati M, which is also co-authored by someone with
the same incomplete abbreviation as Dr. Khan
Q3. On the results page, you will see two tabs, “All” and “Review”. What is the
difference between them?
Q4. Is Pubmed comprehensive?
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B) Questions
p53
12 records
total
Both
terms:
5 records
cancer
15 records
total
p53 AND cancer: returns how many records ?
p53 OR cancer: returns how many records ?
p53 NOT cancer: returns how many records ?
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C) Questions
Q1) When you perform a search for P53 in the protein database,
you observe 4 tabs on top, namely All, Bacteria, Refseq and
Related Structures. What do you think is the difference between
“RefSeq” and “All” tab?
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D) Questions
Q1) Using the skills you have learned and databases that have been
introduced to you, can find out where in the p53 protein is the
Nuclear Localization Signal located? i.e., what is the sequence
range?
Q2) Does the entry belong (P04637) to Refseq database? (Hint:
analyze the alphanumeric identifiers of the entry)
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Summary of items covered today
• Intro to Practicals – logistics
• Search strategies exercise and discussion
• Explored basic bioinformatics resources – exercise
and discussion
• Tips/Tricks to improve productivity
• “Libproxy1” suffix shortcut
• WizFolio
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