The document provides instructions for exploring the National Center for Biotechnology Information (NCBI) database. It guides the user through conducting various searches on the NCBI Search portal to find information on a specific Arabidopsis thaliana gene. The searches demonstrate how to effectively query the database using accession numbers, keywords, and organism qualifiers. The results are analyzed to learn details about the gene sequence, protein product, genomic context, and related data available in linked databases at NCBI.
This document discusses biological databases and nucleic acid sequence databases. It describes the three primary nucleotide sequence databases: GenBank, EMBL, and DDBJ. GenBank is hosted by the National Center for Biotechnology Information and contains over 286 million bases and 352,000 sequences. EMBL is hosted by the European Molecular Biology Laboratory and mirrors data daily with GenBank and DDBJ. DDBJ is the DNA Data Bank of Japan and also mirrors data daily with the other two databases. Biological databases are important tools for scientists to understand biology at multiple levels.
Introduction to Gene Mining Part A: BLASTn-off!adcobb
In this lesson, students will learn to use bioinformatics portals and tools to mine plant versions of human genes. Student handout and teacher resource materials are available at www.Araport.org, Teaching Resources (Community tab). Suitable for grades 9-12 or first year undergraduate students.
The DNA Data Bank of Japan (DDBJ) is a biological database that collects DNA sequences. It is located at the National Institute of Genetics (NIG) in the Shizuoka prefecture of Japan. It is also a member of the International Nucleotide Sequence Database Collaboration or INSDC.
The document provides information about various biological sequence databases and bioinformatics tools and resources. It discusses nucleotide sequence databases like GenBank, EMBL, and DDBJ. It also mentions genome-centered databases like NCBI Genomes and Ensembl Genome Browser. Additionally, it covers protein databases like UniProt and PDB. It describes bioinformatics resources at EBI and NCBI like Entrez. Finally, it summarizes tools for sequence retrieval, comparison, and analysis like BLAST, sequence alignment, and genome browsers.
A database is a structured collection of data that can be easily accessed, managed, and updated. It consists of files or tables containing records with fields. Database management systems provide functions like controlling access, maintaining integrity, and allowing non-procedural queries. Major databases include GenBank, EMBL, and DDBJ for nucleotide sequences and UniProt, PDB, and Swiss-Prot for proteins. The NCBI maintains many biological databases and provides tools for analysis.
1. The document introduces biological databases, their features, types and examples. It discusses primary databases that contain original experimental data and secondary databases that add value through integration and annotation.
2. The National Center for Biotechnology Information (NCBI) is described as a major source of biological databases and tools. NCBI databases include GenBank, PubMed, and Entrez which allow integrated searches.
3. Primary databases like GenBank contain original sequence submissions while derivative databases like RefSeq and UniProt add curation and non-redundancy. Databases are increasingly integrated through links and cross-referencing to provide more comprehensive information to
The document discusses several key nucleotide sequence databases:
- DDBJ (DNA Data Bank of Japan) collects and provides freely available nucleotide sequence data as part of the International Nucleotide Sequence Database Collaboration. It is located in Japan.
- NCBI (National Center for Biotechnology Information) hosts many biological databases including GenBank. It is part of the US National Library of Medicine.
- EMBL (European Molecular Biology Laboratory) is a molecular biology research organization supported by European countries. It operates several sites including the European Bioinformatics Institute which hosts the EMBL-Bank nucleotide sequence database.
This document discusses biological databases and nucleic acid sequence databases. It describes the three primary nucleotide sequence databases: GenBank, EMBL, and DDBJ. GenBank is hosted by the National Center for Biotechnology Information and contains over 286 million bases and 352,000 sequences. EMBL is hosted by the European Molecular Biology Laboratory and mirrors data daily with GenBank and DDBJ. DDBJ is the DNA Data Bank of Japan and also mirrors data daily with the other two databases. Biological databases are important tools for scientists to understand biology at multiple levels.
Introduction to Gene Mining Part A: BLASTn-off!adcobb
In this lesson, students will learn to use bioinformatics portals and tools to mine plant versions of human genes. Student handout and teacher resource materials are available at www.Araport.org, Teaching Resources (Community tab). Suitable for grades 9-12 or first year undergraduate students.
The DNA Data Bank of Japan (DDBJ) is a biological database that collects DNA sequences. It is located at the National Institute of Genetics (NIG) in the Shizuoka prefecture of Japan. It is also a member of the International Nucleotide Sequence Database Collaboration or INSDC.
The document provides information about various biological sequence databases and bioinformatics tools and resources. It discusses nucleotide sequence databases like GenBank, EMBL, and DDBJ. It also mentions genome-centered databases like NCBI Genomes and Ensembl Genome Browser. Additionally, it covers protein databases like UniProt and PDB. It describes bioinformatics resources at EBI and NCBI like Entrez. Finally, it summarizes tools for sequence retrieval, comparison, and analysis like BLAST, sequence alignment, and genome browsers.
A database is a structured collection of data that can be easily accessed, managed, and updated. It consists of files or tables containing records with fields. Database management systems provide functions like controlling access, maintaining integrity, and allowing non-procedural queries. Major databases include GenBank, EMBL, and DDBJ for nucleotide sequences and UniProt, PDB, and Swiss-Prot for proteins. The NCBI maintains many biological databases and provides tools for analysis.
1. The document introduces biological databases, their features, types and examples. It discusses primary databases that contain original experimental data and secondary databases that add value through integration and annotation.
2. The National Center for Biotechnology Information (NCBI) is described as a major source of biological databases and tools. NCBI databases include GenBank, PubMed, and Entrez which allow integrated searches.
3. Primary databases like GenBank contain original sequence submissions while derivative databases like RefSeq and UniProt add curation and non-redundancy. Databases are increasingly integrated through links and cross-referencing to provide more comprehensive information to
The document discusses several key nucleotide sequence databases:
- DDBJ (DNA Data Bank of Japan) collects and provides freely available nucleotide sequence data as part of the International Nucleotide Sequence Database Collaboration. It is located in Japan.
- NCBI (National Center for Biotechnology Information) hosts many biological databases including GenBank. It is part of the US National Library of Medicine.
- EMBL (European Molecular Biology Laboratory) is a molecular biology research organization supported by European countries. It operates several sites including the European Bioinformatics Institute which hosts the EMBL-Bank nucleotide sequence database.
The document provides information about bioinformatics and BLAST (Basic Local Alignment Search Tool). It defines bioinformatics as the application of information technology to molecular biology. It describes what BLAST is and how it works to compare biological sequences and identify similar sequences in databases. It also lists different BLAST programs and databases that can be used depending on the type of sequence being searched.
one complete report from all the 4 labs.pdfstudy help
The document provides instructions for compiling a complete lab report from four biology labs on genomic databases, primer design, PCR, and molecular cloning. It outlines the necessary sections for the report, including an introduction describing the overall question and background, materials and methods, results with data and figures, and a discussion/conclusion section. It also provides additional details on designing a transgene reporter gene based on knowledge gained from the lab exercises, including defining a transgene, necessary gene elements, and ideas for using the transgene.
one complete report from all the 4 labs.pdfstudy help
The document provides instructions for compiling a complete lab report from four biology labs on genomic databases, primer design, PCR, and molecular cloning. It outlines the required sections of the report, including an introduction, materials and methods, results with data, and a discussion/conclusion section. It also provides discussion questions on building a reporter gene or transgene, defining key terms and outlining the necessary gene elements and ideas for using the transgene. The report should integrate results and instructions from all four labs.
This is a tutorial for the sol genomics network (sgn; http://sgn.cornell.edu/) community annotation database. It guides users step-by-step how to access the locus and phenotype database, search for genes and phenotypes, and annotate online using a simple, shared, web interface.
This document provides an introduction to biological databases. It discusses what databases are and features of an ideal database. It describes the relationships between primary sequence databases like GenBank that contain original submissions, and derived databases like RefSeq that are curated by NCBI. Key databases at NCBI are described, including GenBank, RefSeq, and Entrez, which allows integrated searching across multiple databases. The benefits of data integration through linking related information are highlighted.
This document provides an introduction to biological databases. It discusses primary databases like GenBank which contain original sequence submissions and secondary databases derived from primary data, maintained by third parties like NCBI. Some key databases mentioned include GenBank, PDB, Swiss-Prot. The document also provides an overview of the NCBI and Entrez retrieval system, which allows integrated searches across literature and sequences.
Prototype Crop Wild Relatives Portal, at the IMC Meeting (2007)Dag Endresen
The document summarizes a portal for accessing data on crop wild genetic resources. It describes the data sources and partners involved, the data sharing software and structure, features of the portal including searching, viewing metadata and results, and contact information. It also outlines plans to integrate mapping and improve compatibility with biodiversity standards.
1
Phylogenetic Analysis Homework assignment
This assignment will be completed on your own and turned in the week of 11/8-11/10.
Introduction
Molecular evolution is the study of how proteins and nucleic acids evolve. Included in this
field are studies of mutations and chromosomal rearrangements, the evolutionary process,
the identification of sequence patterns conferring function in proteins and nucleic acids,
and the reconstruction of the evolutionary history of organisms and the molecules that
they make. All of these studies rely on comparisons of nucleotide or amino acid sequences.
In this tutorial, you will be introduced to some of the fundamental principles of molecular
evolution and the types of bioinformatics tools that are used in evolutionary studies. We
will begin by carrying out a manual sequence comparison, so that the basic concepts can
be introduced, and the remainder of the project will be carried out at The Biology
Workbench, a set of bioinformatics analysis programs managed by The San Diego
Supercomputing Center at the University of California, San Diego.
Objectives
• To introduce the principles of molecular evolution
• To acquaint you with the tools that are available to compare nucleotide and
amino acid sequences
• To learn about the use of protein sequences in reconstructions of evolutionary history
Project
Branching evolution occurs when one ancestral species gives rise to two or more progeny
species. However, speciation events don't involve the vast majority of the genes in a
genome. That is, for most genes, both of the progeny species inherit identical genes from
the ancestor. Following speciation, these genes evolve independently in the separate
lineages. Studies of molecular evolution therefore rely heavily on comparisons of related
sequences from different organisms.
Shown below is an alignment of two homologous sequences that we will use as a starting
place. Homologous sequences are sequences that have descended from a common
ancestral sequence. You can't meaningfully compare sequences unless they are
homologous. This alignment uses the single letter amino acid code, in which G represents
glycine, Q represents glutamine, etc. The aligned proteins have been shown to be involved
in the metabolism of similar, but different, toxic compounds. As you can see, these amino
acid sequences are very similar and it is easy to recognize that they are related by common
descent.
2
dntAc: KMGVDDEVIVSRQNDGSVR
nahAc: KMGIDDEVIVSRQSDGSIR
An expanded version of this alignment is shown below. In this expanded alignment, both
the amino acids and the corresponding DNA nucleotides are shown. For ease of analysis,
the codons have been broken into separate entries in a table.
Alignment of nahAc and dntAc sequences.
K M G V D E V I V
dntAc AAA ATG GGC GTC GAT GAA GTC ATC GTC
nahAc ...
This document discusses major biological databases. It describes three types of biological databases: primary databases that contain original experimental data, secondary databases that contain additional derived information from primary databases, and composite databases that combine data from multiple sources. The document focuses on describing GenBank, a primary sequence database maintained by the National Center for Biotechnology Information. It provides details on how sequences are submitted to GenBank and how entries are formatted, including information contained in various fields like LOCUS, DEFINITION, and FEATURES. The document also briefly introduces the European Molecular Biology Laboratory database, EMBL, which collaborates with GenBank and DDBJ to exchange nucleotide sequence data daily.
Lesson13: Searching Library Databases Using OneSearchdachterman
The document provides instructions for refining searches in a library database. It recommends starting with a broad search and gradually narrowing the search terms based on what the initial results show. Key steps include learning from the initial results, keeping a list of new search terms found, and using subject terms and advanced search features to narrow the results. The document also explains how to evaluate results lists and find full-text articles.
Finding Information on your Research Topic Searching Academic Search Complete...kerasmus
The document provides steps for finding information for research using the UWC library resources. It discusses accessing the library website and searching databases like EbscoHost. It describes setting up a personal EbscoHost account to save searches and alerts. It also outlines using the Full Text Finder to access specific journal articles, and requesting items through Inter-library Loans that are not available in the UWC library collection.
Finding information on your nursing research topickerasmus
The document provides steps for finding information for research using the UWC library resources. It discusses accessing the library website and searching databases like EbscoHost. It describes setting up a personal EbscoHost account to save searches and alerts. It also outlines using the Full Text Finder to access specific journal articles, and requesting items through Inter-library Loans that are not available in the UWC library collection.
This document provides guidance on conducting research for a capstone project. It outlines how to access library databases remotely, select relevant databases, and limit searches. It recommends specific education databases from EBSCO and ProQuest. Tips are provided on identifying articles with quantitative data and finding full text when only an abstract is available. Formatting references in APA style is also addressed, with suggestions to use library guides, online help or citation management software. Contact information is provided for research assistance.
The document discusses the Rice Annotation Project Database (RAP-DB), which provides annotation of the rice genome sequence. RAP-DB was created in 2004 after the rice genome was sequenced. Its main objective is comprehensive analysis of rice genome structure and function based on annotation. RAP-DB contains tools like BLAST, BLAT, and ID converter to allow users to search and analyze rice genes and genomes. It also contains GBrowse, which allows users to browse rice genes and view their precise locations and other details. Additional features include downloads, publications, links to other rice resources, and documentation.
This document discusses various bioinformatics tools and their functions. It provides details on multiple sequence alignment tools like CLUSTAL Omega, CLUSTALW, BLAST, and FASTA. It explains that CLUSTAL Omega can align a large number of sequences quickly and accurately using progressive alignment. CLUSTALW performs multiple sequence alignment in three steps - pairwise alignment, guide tree creation, and multiple alignment using the guide tree. BLAST can identify unknown sequences by comparing them to known sequences. FASTA uses short exact matches to find similar regions between sequences. Expasy provides access to databases for proteomics, genomics, and other areas. MASCOT searches peptide mass fingerprinting and shotgun proteomics datasets.
This tutorial provides an overview of the key features and search functions of the CINAHL database. It demonstrates how to use the publications, headings, evidence-based care sheets and cited references sections. It also explains the benefits of creating a user account, such as saving searches and setting up alerts. The tutorial highlights using advanced search techniques for effective research.
Genomic databases are public repositories that store genomic data. The three main nucleic acid databases are GenBank at the National Center for Biotechnology Information (NCBI), the European Nucleotide Archive (ENA) at the European Bioinformatics Institute (EBI), and the DNA Data Bank of Japan (DDBJ). These databases synchronize daily to provide comprehensive nucleotide sequence data. GenBank can be queried using tools like BLAST or Entrez to search for sequences and annotations. There are also specialized genomic databases focused on specific organisms like FlyBase for Drosophila or PomBase for fission yeast.
This document provides instructions for experiments involving bioinformatics tools and software. It begins with introductory information and a table of contents. The experiments cover topics like downloading sequences from NCBI, performing BLAST searches, converting between protein and nucleotide sequences, downloading and using MEGA and other software for phylogenetic analysis, primer design, sequence cleaning and formatting, and more. Step-by-step instructions are provided for completing each analysis using various online and offline bioinformatics resources.
Adhd Medication Shortage Uk - trinexpharmacy.comreignlana06
The UK is currently facing a Adhd Medication Shortage Uk, which has left many patients and their families grappling with uncertainty and frustration. ADHD, or Attention Deficit Hyperactivity Disorder, is a chronic condition that requires consistent medication to manage effectively. This shortage has highlighted the critical role these medications play in the daily lives of those affected by ADHD. Contact : +1 (747) 209 – 3649 E-mail : sales@trinexpharmacy.com
The document provides information about bioinformatics and BLAST (Basic Local Alignment Search Tool). It defines bioinformatics as the application of information technology to molecular biology. It describes what BLAST is and how it works to compare biological sequences and identify similar sequences in databases. It also lists different BLAST programs and databases that can be used depending on the type of sequence being searched.
one complete report from all the 4 labs.pdfstudy help
The document provides instructions for compiling a complete lab report from four biology labs on genomic databases, primer design, PCR, and molecular cloning. It outlines the necessary sections for the report, including an introduction describing the overall question and background, materials and methods, results with data and figures, and a discussion/conclusion section. It also provides additional details on designing a transgene reporter gene based on knowledge gained from the lab exercises, including defining a transgene, necessary gene elements, and ideas for using the transgene.
one complete report from all the 4 labs.pdfstudy help
The document provides instructions for compiling a complete lab report from four biology labs on genomic databases, primer design, PCR, and molecular cloning. It outlines the required sections of the report, including an introduction, materials and methods, results with data, and a discussion/conclusion section. It also provides discussion questions on building a reporter gene or transgene, defining key terms and outlining the necessary gene elements and ideas for using the transgene. The report should integrate results and instructions from all four labs.
This is a tutorial for the sol genomics network (sgn; http://sgn.cornell.edu/) community annotation database. It guides users step-by-step how to access the locus and phenotype database, search for genes and phenotypes, and annotate online using a simple, shared, web interface.
This document provides an introduction to biological databases. It discusses what databases are and features of an ideal database. It describes the relationships between primary sequence databases like GenBank that contain original submissions, and derived databases like RefSeq that are curated by NCBI. Key databases at NCBI are described, including GenBank, RefSeq, and Entrez, which allows integrated searching across multiple databases. The benefits of data integration through linking related information are highlighted.
This document provides an introduction to biological databases. It discusses primary databases like GenBank which contain original sequence submissions and secondary databases derived from primary data, maintained by third parties like NCBI. Some key databases mentioned include GenBank, PDB, Swiss-Prot. The document also provides an overview of the NCBI and Entrez retrieval system, which allows integrated searches across literature and sequences.
Prototype Crop Wild Relatives Portal, at the IMC Meeting (2007)Dag Endresen
The document summarizes a portal for accessing data on crop wild genetic resources. It describes the data sources and partners involved, the data sharing software and structure, features of the portal including searching, viewing metadata and results, and contact information. It also outlines plans to integrate mapping and improve compatibility with biodiversity standards.
1
Phylogenetic Analysis Homework assignment
This assignment will be completed on your own and turned in the week of 11/8-11/10.
Introduction
Molecular evolution is the study of how proteins and nucleic acids evolve. Included in this
field are studies of mutations and chromosomal rearrangements, the evolutionary process,
the identification of sequence patterns conferring function in proteins and nucleic acids,
and the reconstruction of the evolutionary history of organisms and the molecules that
they make. All of these studies rely on comparisons of nucleotide or amino acid sequences.
In this tutorial, you will be introduced to some of the fundamental principles of molecular
evolution and the types of bioinformatics tools that are used in evolutionary studies. We
will begin by carrying out a manual sequence comparison, so that the basic concepts can
be introduced, and the remainder of the project will be carried out at The Biology
Workbench, a set of bioinformatics analysis programs managed by The San Diego
Supercomputing Center at the University of California, San Diego.
Objectives
• To introduce the principles of molecular evolution
• To acquaint you with the tools that are available to compare nucleotide and
amino acid sequences
• To learn about the use of protein sequences in reconstructions of evolutionary history
Project
Branching evolution occurs when one ancestral species gives rise to two or more progeny
species. However, speciation events don't involve the vast majority of the genes in a
genome. That is, for most genes, both of the progeny species inherit identical genes from
the ancestor. Following speciation, these genes evolve independently in the separate
lineages. Studies of molecular evolution therefore rely heavily on comparisons of related
sequences from different organisms.
Shown below is an alignment of two homologous sequences that we will use as a starting
place. Homologous sequences are sequences that have descended from a common
ancestral sequence. You can't meaningfully compare sequences unless they are
homologous. This alignment uses the single letter amino acid code, in which G represents
glycine, Q represents glutamine, etc. The aligned proteins have been shown to be involved
in the metabolism of similar, but different, toxic compounds. As you can see, these amino
acid sequences are very similar and it is easy to recognize that they are related by common
descent.
2
dntAc: KMGVDDEVIVSRQNDGSVR
nahAc: KMGIDDEVIVSRQSDGSIR
An expanded version of this alignment is shown below. In this expanded alignment, both
the amino acids and the corresponding DNA nucleotides are shown. For ease of analysis,
the codons have been broken into separate entries in a table.
Alignment of nahAc and dntAc sequences.
K M G V D E V I V
dntAc AAA ATG GGC GTC GAT GAA GTC ATC GTC
nahAc ...
This document discusses major biological databases. It describes three types of biological databases: primary databases that contain original experimental data, secondary databases that contain additional derived information from primary databases, and composite databases that combine data from multiple sources. The document focuses on describing GenBank, a primary sequence database maintained by the National Center for Biotechnology Information. It provides details on how sequences are submitted to GenBank and how entries are formatted, including information contained in various fields like LOCUS, DEFINITION, and FEATURES. The document also briefly introduces the European Molecular Biology Laboratory database, EMBL, which collaborates with GenBank and DDBJ to exchange nucleotide sequence data daily.
Lesson13: Searching Library Databases Using OneSearchdachterman
The document provides instructions for refining searches in a library database. It recommends starting with a broad search and gradually narrowing the search terms based on what the initial results show. Key steps include learning from the initial results, keeping a list of new search terms found, and using subject terms and advanced search features to narrow the results. The document also explains how to evaluate results lists and find full-text articles.
Finding Information on your Research Topic Searching Academic Search Complete...kerasmus
The document provides steps for finding information for research using the UWC library resources. It discusses accessing the library website and searching databases like EbscoHost. It describes setting up a personal EbscoHost account to save searches and alerts. It also outlines using the Full Text Finder to access specific journal articles, and requesting items through Inter-library Loans that are not available in the UWC library collection.
Finding information on your nursing research topickerasmus
The document provides steps for finding information for research using the UWC library resources. It discusses accessing the library website and searching databases like EbscoHost. It describes setting up a personal EbscoHost account to save searches and alerts. It also outlines using the Full Text Finder to access specific journal articles, and requesting items through Inter-library Loans that are not available in the UWC library collection.
This document provides guidance on conducting research for a capstone project. It outlines how to access library databases remotely, select relevant databases, and limit searches. It recommends specific education databases from EBSCO and ProQuest. Tips are provided on identifying articles with quantitative data and finding full text when only an abstract is available. Formatting references in APA style is also addressed, with suggestions to use library guides, online help or citation management software. Contact information is provided for research assistance.
The document discusses the Rice Annotation Project Database (RAP-DB), which provides annotation of the rice genome sequence. RAP-DB was created in 2004 after the rice genome was sequenced. Its main objective is comprehensive analysis of rice genome structure and function based on annotation. RAP-DB contains tools like BLAST, BLAT, and ID converter to allow users to search and analyze rice genes and genomes. It also contains GBrowse, which allows users to browse rice genes and view their precise locations and other details. Additional features include downloads, publications, links to other rice resources, and documentation.
This document discusses various bioinformatics tools and their functions. It provides details on multiple sequence alignment tools like CLUSTAL Omega, CLUSTALW, BLAST, and FASTA. It explains that CLUSTAL Omega can align a large number of sequences quickly and accurately using progressive alignment. CLUSTALW performs multiple sequence alignment in three steps - pairwise alignment, guide tree creation, and multiple alignment using the guide tree. BLAST can identify unknown sequences by comparing them to known sequences. FASTA uses short exact matches to find similar regions between sequences. Expasy provides access to databases for proteomics, genomics, and other areas. MASCOT searches peptide mass fingerprinting and shotgun proteomics datasets.
This tutorial provides an overview of the key features and search functions of the CINAHL database. It demonstrates how to use the publications, headings, evidence-based care sheets and cited references sections. It also explains the benefits of creating a user account, such as saving searches and setting up alerts. The tutorial highlights using advanced search techniques for effective research.
Genomic databases are public repositories that store genomic data. The three main nucleic acid databases are GenBank at the National Center for Biotechnology Information (NCBI), the European Nucleotide Archive (ENA) at the European Bioinformatics Institute (EBI), and the DNA Data Bank of Japan (DDBJ). These databases synchronize daily to provide comprehensive nucleotide sequence data. GenBank can be queried using tools like BLAST or Entrez to search for sequences and annotations. There are also specialized genomic databases focused on specific organisms like FlyBase for Drosophila or PomBase for fission yeast.
This document provides instructions for experiments involving bioinformatics tools and software. It begins with introductory information and a table of contents. The experiments cover topics like downloading sequences from NCBI, performing BLAST searches, converting between protein and nucleotide sequences, downloading and using MEGA and other software for phylogenetic analysis, primer design, sequence cleaning and formatting, and more. Step-by-step instructions are provided for completing each analysis using various online and offline bioinformatics resources.
Adhd Medication Shortage Uk - trinexpharmacy.comreignlana06
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The skin is the largest organ and its health plays a vital role among the other sense organs. The skin concerns like acne breakout, psoriasis, or anything similar along the lines, finding a qualified and experienced dermatologist becomes paramount.
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It is mostly found in the brain, intestines, and blood platelets.
5-HT is utilised to transport messages between nerve cells, is known to be involved in smooth muscle contraction, and adds to overall well-being and pleasure, among other benefits. 5-HT regulates the body's sleep-wake cycles and internal clock by acting as a precursor to melatonin.
It is hypothesised to regulate hunger, emotions, motor, cognitive, and autonomic processes.
Mercurius is named after the roman god mercurius, the god of trade and science. The planet mercurius is named after the same god. Mercurius is sometimes called hydrargyrum, means ‘watery silver’. Its shine and colour are very similar to silver, but mercury is a fluid at room temperatures. The name quick silver is a translation of hydrargyrum, where the word quick describes its tendency to scatter away in all directions.
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Bioinformatics Lab01.docx
1. LAB 1 EXPLORING NCBI
[Software needed: web access]
The National Center for Biotechnology Information (NCBI) maintained by the US National
Library of Medicine and National Institutes of Health is one of the world’s most important
resources and repositories for biological data. This fantastic online resource provides an
extensive network of databases cataloging an ever-growing wealth of genetic, medical, and
biochemical information from all walks and crawls of life. Entire genomes, from viruses to
humans, are compiled, organized, and cross-referenced within these networks, such that surfing
the genome can be almost as easy as surfing the web.
But you have to know a) what you’re looking for, and b) what you’re looking at to get anything
out of these databases. This is what this first lab is going to help you do. Note that Google and
other search engines typically do not index database-driven websites, which is why it cannot be
used for searching for information that is stored at NCBI (nor does it handle sequence searching
well, especially in the case of protein sequences).
The primary portal for accessing data at NCBI is called Search NCBI. But first, let’s start by
visiting NCBI’s website and examining the interface, which undergoes constant change.
1. Open your Web browser and go to NCBI’s homepage: www.ncbi.nlm.nih.gov. This page
provides links to all of NCBI databases and resources. It’s worth exploring here just to
get a better idea of the scope of NCBI. If you click About the NCBI you will be taken to
a page summarizing some of these resources. You can also check out the NCBI
Handbook (http://www.ncbi.nlm.nih.gov/books/NBK21101/) for more information.
Figure 1. The NCBI homepage.
2. 2. Now let’s move to the Search NCBI (formerly known as GQuery or Entrez) portal – select
All Databases from the navigation bar at the top of the NCBI start page and click “Search”
beside the empty field. First, scan down the assortment of databases queried through this
portal. You will notice there is everything from the biomedical literature at PubMed to
nucleotide databases, taxonomy databases, protein structure databases, and expression profile
databases. Let’s see what happens when you do an unguided search on the site. In the
"Search NCBI" box, type in bacteria. The output is a summary page of the number of hits in
each section. A search of bacteria gives millions of hits – not very helpful. We need
specifics.
Figure 2. The Search NCBI portal page with bacteria used as a search word.
3. Usually when searching these databases, you have either a region of DNA or a protein (or
protein function) of interest. For this lab you’ll be using a gene from Arabidopsis
thaliana, a small flowering plant that is like the fruit fly of the plant world as it has a
comparatively rapid life cycle and requires little space to grow. The protein product of
this gene is recorded under accession number NP_001318308, and it is an E3 ligase,
involved in ubiquitination of proteins, which is a signal for their degradation.
3.
Box 1. Accession Numbers and Version Numbers (and GI Numbers…)
An Accession number is a unique identifier for a particular sequence record. An accession
number is assigned to a specific record and stays with that record forever. In other words,
Accession numbers track a particular record and do not change even if the information in the
record is changed at the author's request (e.g. if a better annotation or more complete sequence
is provided). Accession numbers are usually a combination of a letter(s) and numbers, such as a
single letter followed by five digits (e.g., U12345) or two letters followed by six digits (e.g.,
AF123456).
Version numbers follow the Accession number and indicate the revision history of that entry
starting with 1 and increasing with each revision. The standard format is Accession.Version.
A GI number (GenInfo Identifier – sometimes written in lower case, "gi") was simply a series
4. Go back to the Search NCBI portal page and try a more focused search. Use the search terms
found associated with the gene sequence we’ll be using with the GenBank Field Qualifiers
shown below (a full list of qualifiers is presented in Appendix 1). Try the four different
searches presented below and look at the number records, specifically “Protein” records,
found:
gene keywords
e.g. ubiquitin-protein ligase
gene keyword AND organism
e.g. ubiquitin-protein ligase AND Arabidopsis thaliana
gene keyword [PROT] AND organism [ORGN]
e.g. ubiquitin-protein ligase [PROT] AND Arabidopsis thaliana [ORGN]
accession or GI number
e.g. NP_001318308
That narrowed things down significantly!
Note that using parentheses can be very helpful in making sure you get exactly what you
want. For example:
SMC AND (yeast [ORGN] OR Arabidopsis [ORGN])
is a very different search than
SMC AND yeast [ORGN] OR Arabidopsis [ORGN]
Also, using quotation marks can also dramatically affect your search (ie: 16s rRNA vs. “16s
rRNA”).
Finally, always capitalize the Boolean operators such as AND / OR / NOT.
Ultimately, the most specific search items you can use are accession numbers.
4. Box 2. NCBI Help
This is a good time to get familiar with NCBI’s thorough Help index for future reference. With
this index, you should be able to access most of the background you need for understanding
how these databases work on your own (there’s also an NCBI YouTube channel if you’d like to
check that out too).
1. At the bottom left of the NCBI homepage find the “NCBI Help Manual” link.
Click on it. Then access the “Entrez Help” section.
2. You are now in Entrez Help. The Entrez collection of databases is queried when you use
the Search NCBI interface. Note the contents that explain everything from search options
to saving sets of records.
3. Notice that under the section Entrez Searching Options some other appropriate
qualifiers are given, as illustrated on the previous page.
5. Search for our accession number of interest (e.g. NP_001318308 from above) through the
Search NCBI portal page. It should give you 1 protein sequence hit. Click on it (it is a
hyperlink) so that you get its full GenBank description (you can also click on the
“armadillo/beta-catenin repeat protein [Arabidopsis thaliana]” link at the top of the page
as the NCBI system recognizes that you’ve entered a protein identifier and hence
provides some summary information for that above the numerical overview of results).
of digits that was, until recently, assigned consecutively to each sequence record processed by
NCBI. The GI system of identifiers ran in parallel to the Accession.Version system; therefore, if
the DNA or protein sequence changed in any way, it would receive a new GI number.
Example: When a new entry was submitted to GenBank it was assigned an accession number
(say AF000001). Since this is the first version the Accession would be appended with ‘.1’, so it
would look like AF000001.1. At the same time was given a GI number (say GI:1234567). Now
imagine that the researcher who originally submitted the record wanted to update the
information. The updated record would keep the same Accession number, but would increase in
version number (AF000001.2). The new record would have been given a completely new GI
number (say GI:9876543).
Why is this important? The Accession number will always give you the most up-to-date
information on a record, while the Accession.Version will always take you to a specific record.
There are times when you want the most current information, and other times when you want to
point to a particular piece of information from a particular point in time (e.g. a particular record
that you did an analysis with), even if more information has been subsequently added. Note that
as of September 2016, NCBI started phasing out the use of GI numbers. The use of
Accession.Version form is now recommended for accessing a particular record, instead of the
GI number. GI numbers are not to be confused with Entrez Gene IDs, which are another
referencing system that NCBI uses entirely!
5. Figure 3. GenBank record for accession NP_001318308, in GenPept format.
6. 6. Notice all the hyperlinks within the text. It looks messy but is in fact straightforward. For
example, for taxonomic information, click on the SOURCE ORGANISM hyperlink. Some
records have links to the primary publication where this sequence was originally cited in a
PUBMED number hyperlink (not the case in the above example, but there is a PubMed
reference for the sequence). Click around on different links and see what you find.
a. What is the taxonomic lineage of your organism?
b. Has the genome of this organism been sequenced, i.e. is there a Genome Project?
c. If so, can you find the accession for the full sequence or one of the chromosomes?
To find out much more information on the structure of the GenBank file at
http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html
7. Go back to the GenBank record and click on the CDS link, just above the actual sequence
(circled in red in Figure 3 on the previous page).
a. Where did this take you or what happened when you did this?
8. Go back to the GenBank record and examine the Related Information section on the lower
right. This gives you direct links to other databases with information on this query. Find the
Gene link.
Figure 4. The Related Information menu for NP_001318308, to the right of the record. The
arrow is pointing to the “Gene” link.
9. Select Gene from the Related Information menu. This is a great starter resource at NCBI.
Scroll through the different sections. Use them to answer the following questions.
a. Where is your gene’s location in the genome? (Tip: hover with your cursor over the
green bars in the “Genomic regions, transcripts, and products” section; the green
bars represent the gene in the sequence viewer)
b. How many exons do you see in this gene? Tip: how many green boxes are there?
c. What are the names of the genes surrounding it (i.e. what is its “Genomic context”)?
d. Does it have any conserved domains? What are they called? (Tip: use the “Related
Information” link to Conserved Domains on the right of the Gene page)
7. e. After exploring conserved domains go back to the Gene page. What biological
process (Gene Ontology terms) is this gene involved with (scroll down!)?
Figure 5. GenBank Gene page for At2g28830 (also known as PUB12), the gene that encodes
NP_001318308.
10. On the Gene page, there are also Additional links to examine a gene’s structure, function
and phylogenetic relationships further. The navigation sidebar on the right has an
“Additional links” hyperlink which will take you to the bottom of the page, where they’re
found for most genes. Click [+] Gene LinkOut to see them.
a. Click on Additional Links. What kind of information is in this section?
8. Click around and explore the variety of ways that data for PUB12 are interconnected and
displayed (don’t worry, you can’t break anything). Using the Related Information links
can you find any publications associated with this gene? What about gene expression
data? The next page shows the related “RefSeq RNA” record for the corresponding
encoding mRNA (NCBI’s RefSeq aims to provide canonical “reference” sequences –
genomic, mRNA, CDS, protein etc. – for many model organisms).
b.Why is the length of the mRNA different from the value you can calculate from the start
and stop positions in Question 9a?
Figure 6. RefSeq RNA linked from Gene page for At2g28830
9. Box 3. Helpful Hints for NCBI searches
On most NCBI search pages (except, oddly, Search NCBI) click on “Save Search” or “Create
Alert” below the search box. Register for an account and save your search. You can also
combine previous searches using the History tab and the search numbers listed within it, as
well as save your searches by registering for a My NCBI account, so you don’t have to keep
redoing the same searches in the future.