Searching the NCBI Databases

Slides:



Advertisements
Similar presentations
Bioinformatics growth curves Medline records Computer power DNA sequences 3-D structures.
Advertisements

Submitting a Genome to RAST. Uploading Your Job 1.Login to your RAST account. You will need to register if this is your first time using SEED technologies.
What is RefSeqGene?.
Integrating dbSNP with P. falciparum genome resources.
Integration of Protein Family, Function, Structure Rich Links to >90 Databases Value-Added Reports for UniProtKB Proteins iProClass Protein Knowledgebase.
1 Introduction to Bioinformatics Fall Administration  Adi Doron  Nimrod Rubinstein  Dudu Burstein.
Tutorial 7 Genome browser. Free, open source, on-line broswer for genomes Contains ~100 genomes, from nematodes to human. Many tools that can be used.
Practice retrieving data and running stand alone BLAST. Step 1. Identify genes in the ABA biosynthesis pathway from the Arabidopsis Cyc database
Lecture 2.21 Retrieving Information: Using Entrez.
UCSC Archaeal genome browser Advanced browsing September 19, 2006 David Bernick, Aaron Cozen and Todd Lowe September 19, 2006 David Bernick, Aaron Cozen.
UCSC Genome Browser Tutorial
Biological Databases Notes adapted from lecture notes of Dr. Larry Hunter at the University of Colorado.
Data Mining in Ensembl with EnsMart. 2 of 24 All genes from a candidate region Genes with a particular protein domain Members of a protein family Genes.
Genome Browsers Ensembl (EBI, UK) and UCSC (Santa Cruz, California)
Genomic Database - Ensembl Ka-Lok Ng Department of Bioinformatics Asia University.
MICB 405 Bioinformatics Mini-Lab #2 - BLAST Dr. Joanne Fox We gratefully acknowledge the funding for the development of these teaching.
Genome Browsing with the UCSC Genome Browser
Asteraceae (Compositae) Genome Resources at NCBI GenBank.
Mutations Section 12–4 This section describes and compares gene mutations and chromosomal mutations.
Arabidopsis Gene Project GK-12 April Workshop Karolyn Giang and Dr. Mulligan.
DbSNP: the NCBI database of genetic variation S. T. Sherry, M.H. Ward, M. Kholodov, J. Baker, L. Phan, E. M. Smigielski and K. Sirotkin, Nucleic Acids.
Python programs How can I run a program? Input and output.
Pathway Assignments. The assignment – Annotating Pathways KEGG Pathway Database.
NCBI’s Bioinformatics Resources Michele R. Tennant, Ph.D., M.L.I.S. Health Science Center Libraries U.F. Genetics Institute January 2015.
Searching PubMed® NCBI, NLM Resources, Micromedex -GSBS TTUHSC Preston Smith Library presents Rev. 08/17/14.
UCSC Genome Browser 1. The Progress 2 Database and Tool Explosion : 230 databases and tools 1996 : first annual compilation of databases and tools.
Organizing information in the post-genomic era The rise of bioinformatics.
Biological databases Exercises. Discovery of distinct sequence databases using ensembl.
NCBI Literature Databases: PubMed
The Reference Sequence database A non-redundant collection of richly annotated DNA, RNA, and protein sequences from diverse taxaDNARNA The collection includes.
GVS: Genome Variation Server Materials prepared by: Warren C. Lathe, PhD Updated: Q Version 2.
Application of Bioinformatics in Genetic Research Instructors: Dr. Henry Baker Dr. Luciano Brocchieri Dr. Michele Tennant Dr. Lei Zhou
Primary vs. Secondary Databases Primary databases are repositories of “raw” data. These are also referred to as archival databases. -This is one of the.
3DM: Protein Super-family Platforms 3DM Protein super-family data integration Tom van den Bergh Bio-Prodict.
Copyright OpenHelix. No use or reproduction without express written consent1.
Copyright OpenHelix. No use or reproduction without express written consent1.
Getting GO: how to get GO for functional modeling Iowa State Workshop 11 June 2009.
Tools in Bioinformatics Genome Browsers. Retrieving genomic information Previous lesson(s): annotation-based perspective of search/data Today: genomic-based.
Genomes at NCBI. Database and Tool Explosion : 230 databases and tools 1996 : first annual compilation of databases and tools lists 57 databases.
Visualization of genomic data Genome browsers. UCSC browser Ensembl browser Others ? Survey.
COURSE OF BIOINFORMATICS Exam_30/01/2014 A.
Welcome to the Protein Database Tutorial. This tutorial will describe how to navigate the section of Gramene that provides collective information on proteins.
Keeping Current: Genetics Resources. This workshop will provide an overview of NCBI resources for finding-- Background information & journal articles.
SC.912.L.16.3 DNA Replication. – During DNA replication, a double-stranded DNA molecule divides into two single strands. New nucleotides bond to each.
Getting GO annotation for your dataset
Introduction to Bioinformatics
CSE 182 Project.
Annotation Presentation
NCBI Molecular Biology Resources
Figure 1. Number of CCDS IDs and genes represented in the human (A) and mouse (B) CCDS releases. The X-axis indicates the year in which a CCDS dataset.
Mutations Chapter 12-4.
What is Bioinformatics?
Pick a Gene Assignment 4 Requirements
GEP Annotation Workflow
Visualization of genomic data
Biological Databases BI420 – Introduction to Bioinformatics
BIOL 3020 GENOMIC BIOLOGY LABORATORY 05A
TAMU Bovine QTL db and viewer
Basic Local Alignment Search Tool
Explore Evolution: Instrument for Analysis
A Tutorial Lincoln Stein, Cold Spring Harbor Laboratory
Nic’s genome contains 16,124 variants,
Genome Biology & Applied Bioinformatics Mehmet Tevfik DORAK, MD PhD
BLAT Blast Like Alignment Tool
Gene Safari (Biological Databases)
Problems from last section
Project BCHB697.
How to search NCBI.
Sequences of two isoforms of Arhgap39/Porf-2 protein in mouse.
Figure 1 Schematic of the OPA3 gene and OPA3 protein isoform b
Presentation transcript:

Searching the NCBI Databases

Search for CFTR[gene] in the Protein database What is it?

Limit to genes in human only CFTR[gene] AND human[orgn] How many?

Restrict to RefSeq How many?

RefSeq records can also be filtered using the Limits tab

Examine the NP_000483 record How many amino-acids are in the protein? On which chromosome is this protein-coding gene located?

Follow the dbSNP link to examine the SNPs associated with this protein How many SNPs?

Follow the dbSNP link to examine the SNPs associated with this protein Describe mutation in first record. Is it synonymous?

Use the Taxonomy Browser to examine fully-sequenced primates genomes

Use the Taxonomy Browser to examine fully-sequenced prototheria genomes

Sequence Retrieval

Search for human BRCA1 in Protein database Select longest isoform

Display the sequences in FASTA format

Save the sequence into a WORD file