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Practical 1

Practical 1. Discussion. Features of major databases (PubMed and NCBI Protein Db). Anatomy of PubMed Db. Epub ahead of print and journal impact factor. How to get impact factor of any journal: Direct source – web of science database

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Practical 1

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  1. Practical 1 Discussion

  2. Features of major databases(PubMed and NCBI Protein Db)

  3. Anatomy of PubMed Db

  4. Epub ahead of print and journal impact factor • How to get impact factor of any journal: • Direct source – web of science database • In direct source, e.g. blogs, sites etc (do Google search) Adopted from : http://admin-apps.isiknowledge.com/JCR/JCR?RQ=LIST_SUMMARY_JOURNAL

  5. Anatomy of a PubMed record

  6. Demo on downloading articles

  7. Anatomy of a Protein Db

  8. Accession numbers and GenInfo Identifiers GI or Geninfo Identifier) 120407067 Refseq database Source NM_000546 Accession NM_000546.3 Version 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

  9. 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?

  10. Why do we need accession number and GI for one record? NM_000546 NM_000546 NM_000546 Sequence update Sequence update Sequence_v3 Sequence_v1 Sequence_v2 NM_000546.3 NM_000546.2 Version NM_000546.1 GI 4507636 120407067 8400737 Q1) Which revision will NCBI show if you were to search by the accession only without the version number?

  11. 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.

  12. 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

  13. 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

  14. Anatomy of a Protein Db record

  15. Fasta Sequence

  16. 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_1 MTEITAAMVKELRESTGAGMMDCKNALSETNGDFDKAVQLLREKGLGKAAKKADRLAAEG LVSVKVSDDFTIAAMRPSYLSYEDLDMTFVENEYKALVAELEKENEERRRLKDPNKPEHK IPQFASRKQLSDAILKEAEEKIKEELKAQGKPEKIWDNIIPGKMNSFIADNSQLDSKLTL MGQFYVMDDKKTVEQVIAEKEKEFGGKIKIVEFICFEVGEGLEKKTEDFAAEVAAQL >SEQUENCE_2 SATVSEINSETDFVAKNDQFIALTKDTTAHIQSNSLQSVEELHSSTINGVKFEEYLKSQI ATIGENLVVRRFATLKAGANGVVNGYIHTNGRVGVVIAAACDSAEVASKSRDLLRQICMH Sequence data line(s) Description line/row Sequence data line(s)

  17. Fasta Format (cont.) • 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_1 MTEITAAMVKELRESTGAGMMDCKNALSETNGDFDKAVQLLREKGLGKAAKKADRLAAEG LVSVKVSDDFTIAAMRPSYLSYEDLDMTFVENEYKALVAELEKENEERRRLKDPNKPEHK IPQFASRKQLSDAILKEAEEKIKEELKAQGKPEKIWDNIIPGKMNSFIADNSQLDSKLTL MGQFYVMDDKKTVEQVIAEKEKEFGGKIKIVEFICFEVGEGLEKKTEDFAAEVAAQL >SEQUENCE_2 SATVSEINSETDFVAKNDQFIALTKDTTAHIQSNSLQSVEELHSSTINGVKFEEYLKSQI ATIGENLVVRRFATLKAGANGVVNGYIHTNGRVGVVIAAACDSAEVASKSRDLLRQICMH Sequence data line(s) Description line/row Sequence data line(s)

  18. Amino acids

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

  20. Note

  21. Advice • 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.

  22. Features of major database (Gene Db)

  23. Anatomy of Gene Db

  24. Anatomy of a Gene Db record

  25. A section of Gene Db record:Reference Sequences mRNA Accession number Protein Accession number

  26. Take home messages for databases • Bioinformatics = databases + tools • General databases versus specialized databases • Databases come and go (especially the small ones) • Database redundancy - many databases for the same topic (use the most comprehensive, if not use all for comprehensiveness) • 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 • Fortunately, most databases are cross-referenced • Unfortunately, no common standard format; need to spend some time familiarizing each; becomes easy after some practice • Finding databases relevant to you • NAR Database catalogue • Pubmed • Google • 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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