Discussion Practical 1 Features of major databases (PubMed in addition to NCBI Protein Db) Anatomy of PubMed Db Epub ahead of print in addition to journal impact factor

Discussion Practical 1 Features of major databases (PubMed in addition to NCBI Protein Db) Anatomy of PubMed Db Epub ahead of print in addition to journal impact factor www.phwiki.com

Discussion Practical 1 Features of major databases (PubMed in addition to NCBI Protein Db) Anatomy of PubMed Db Epub ahead of print in addition to journal impact factor

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Epub ahead of print in addition to 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/JCRRQ=LIST-SUMMARY-JOURNAL Anatomy of a PubMed record Demo on downloading articles

Anatomy of a Protein Db 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 In as long as mation Resource Version NM-000546.3 GI or Geninfo Identifier) 120407067 Source Refseq database Accession NM-000546 Accession numbers in addition to GenInfo Identifiers Why do we need accession number in addition to GI as long as one record 1) What is the difference between accession in addition to GI 2) Why do we need these two when both seem to be accession numbers

Q1) Which revision will NCBI show if you were to search by the accession only without the version number Sequence-v1 NM-000546 Sequence-v2 NM-000546 Sequence-v3 NM-000546 NM-000546.1 NM-000546.2 NM-000546.3 4507636 8400737 120407067 Sequence update Sequence update GI Version Why do we need accession number in addition to GI as long as one record Accession numbers The unique identifier as long as a sequence record. An accession number applies to the complete record. Accession numbers do not change, even if in as long as mation 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 as long as some reason a new submission supercedes an earlier record. 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

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, in addition to update dates as long as sequences that appeared in a specific GenBank record Anatomy of a Protein Db record Fasta Sequence

Fasta Format Text-based as long as mat as long as representing nucleic acid sequences or peptide sequences (single letter codes). Easy to manipulate in addition to parse sequences to programs. >SEQUENCE-1 MTEITAAMVKELRESTGAGMMDCKNALSETNGDFDKAVQLLREKGLGKAAKKADRLAAEG LVSVKVSDDFTIAAMRPSYLSYEDLDMTFVENEYKALVAELEKENEERRRLKDPNKPEHK IPQFASRKQLSDAILKEAEEKIKEELKAQGKPEKIWDNIIPGKMNSFIADNSQLDSKLTL MGQFYVMDDKKTVEQVIAEKEKEFGGKIKIVEFICFEVGEGLEKKTEDFAAEVAAQL >SEQUENCE-2 SATVSEINSETDFVAKNDQFIALTKDTTAHIQSNSLQSVEELHSSTINGVKFEEYLKSQI ATIGENLVVRRFATLKAGANGVVNGYIHTNGRVGVVIAAACDSAEVASKSRDLLRQICMH Description line/row Sequence data line(s) Description line/row Sequence data line(s) 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 “>” in addition to the first letter of the identifier. Keep the identifier short in addition to clear ; Some old programs only accept identifiers of only 10 characters. For example: > gi5524211Human 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. >SEQUENCE-1 MTEITAAMVKELRESTGAGMMDCKNALSETNGDFDKAVQLLREKGLGKAAKKADRLAAEG LVSVKVSDDFTIAAMRPSYLSYEDLDMTFVENEYKALVAELEKENEERRRLKDPNKPEHK IPQFASRKQLSDAILKEAEEKIKEELKAQGKPEKIWDNIIPGKMNSFIADNSQLDSKLTL MGQFYVMDDKKTVEQVIAEKEKEFGGKIKIVEFICFEVGEGLEKKTEDFAAEVAAQL >SEQUENCE-2 SATVSEINSETDFVAKNDQFIALTKDTTAHIQSNSLQSVEELHSSTINGVKFEEYLKSQI ATIGENLVVRRFATLKAGANGVVNGYIHTNGRVGVVIAAACDSAEVASKSRDLLRQICMH Description line/row Sequence data line(s) Description line/row Sequence data line(s) Amino acids

IUPAC One Letter Amino Acid Code 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 Alanine Cysteine Glycine Histidine Isoleucine Leucine Methionine Proline Serine Threonine Valine Glutamic Acid Aspartic Acid Phenylalanine Lysine Asparagine Glutamine Arginine Tryptophan Tyrosine 21st (Sec) Selenocysteine 22nd (Pyl) Pyrrolysine GLx ASx Glutamic Acid Aspar(D)ic Acid (F)enylalanine Lysine Asparagi(N)e (Q)lutamine (R)ginine T(W)ptophan T(Y)rosine 21st (Sec)Selenocysteine 22nd (Pyl) Pyrr(O)lysine GLx ASx Note

Advice We highly recommend that you memorize the amino acid codes in addition to their structures Memorizing the codes in addition to in particular the structures will be very useful as long as this module in addition to other modules, especially as long as research purposes. It is not compulsory that you memorize these as long as this module. Features of major database (Gene Db) Anatomy of Gene Db

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Anatomy of a Gene Db record A section of Gene Db record: Reference Sequences mRNA Accession number Protein Accession number Take home messages as long as databases Bioin as long as matics = databases + tools General databases versus specialized databases Databases come in addition to go (especially the small ones) Database redundancy – many databases as long as the same topic (use the most comprehensive, if not use all as long as 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 Un as long as tunately, no common st in addition to ard as long as mat; 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 as long as searching databases (each with its own pros in addition to cons) 1. Keyword search (covered today) 2. Sequence search (day 2)

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