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Adopted from : http://admin-apps.isiknowledge.com/JCR/JCR?RQ=LIST_SUMMARY_JOURNAL
How to get impact factor of any journal:
1) Direct source – web of science database
2) In direct source, e.g. blogs, sites etc
(do Google search)
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gi| numeric identifier | source | alphanumeric identifier humanP53 RefSeq mRNA record as an example: gi|120407067|ref|NM_000546.3
GI or Geninfo Identifier) 120407067
GI (or GenInfo Identifier) 120407067
Accession
Version
Refseq database
RefSeq database
NM_000546
Other popular 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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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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ACCESSION
NM_000546
GI
VERSION
120407067 NM_000546.3
8400737 NM_000546.2
4507636 NM_000546.1
NM_000546 NM_000546 NM_000546
Version
GI
Sequence_v1
NM_000546.1
4507636
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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- 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 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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- 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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• 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

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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

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• H
• I
• J
• K
• L
• M
• A
• B
• C
• D
• E
• F
• G
Alanine
ASx
Cysteine
Aspar(D)ic Acid
Glutamic Acid
(F)enylalanine
Glycine
Histidine
Isoleucine
Lysine
Leucine
Methionine
• U
• V
• W
• X
• Y
• Z
• N
• O
• P
• Q
• R
• S
• T
Asparagi(N)e
22 nd (Pyl) Pyrr(O)lysine
Proline
(Q)lutamine
(R)ginine
Serine
Threonine
21 st (Sec)Selenocysteine
Valine
T(W)ptophan
T(Y)rosine
GLx
Aspartic Acid
Asparagine
ASx
Arginine
Glutamic Acid
Glutamine
GLx
Lysine
Phenylalanine
Tyrosine
Tryptophan
21 st (Sec) Selenocysteine
22 nd (Pyl) Pyrrolysine

Note
Amino acid
Asparagine or aspartic acid
Glutamine or glutamic acid,
Leucine or Isoleucine,
Unspecified or unknown amino acid
Three letter code Single letter code
Asx B
GLx
Xle
Xaa
Z
J
X

• We highly recommend that you memorize the amino acid codes and their 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.

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Anatomy of a Gene Db record
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mRNA
Accession number
Protein
Accession number
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Bioinformatics = databases + tools
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General databases versus specialized databases
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Databases come and go (especially the small ones)
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Database redundancy - many databases for the same topic (use the most comprehensive, if not use all for comprehensiveness)
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Database accuracy – published ones are more reliable; nevertheless, they are still prone to errors; always good to spend sometime assessing the reliability of your data of interest by doing cross-referencing to literature or other databases
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Fortunately, most databases are cross-referenced
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Unfortunately, no common standard format; need to spend some time familiarizing each; becomes easy after some practice
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Finding databases relevant to you
– NAR Database catalogue
– Pubmed
– Google
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2 main methods for searching databases (each with its own pros and cons)
– 1. Keyword search (covered today)
– 2. Sequence search (day 2)
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