Web-based tools for Bioinformatics; A (free) introduction to

Web-based tools for Bioinformatics; A (free) introduction to (freely available) NCBI, MUSC and World-wide. When and Where---Wednesdays 1pm-2pmRoom 438 Library Admin Building Beginning September 10, 2003.

Overview University of California Santa Cruz Genome Tools November 5, 2003

Introduction/Scope The UCSC Genome Viewer was designed to aid the researcher by providing a graphical interface for examining the human Genome and vast amounts of correlated data. The Genome Browser is similar to those at NCBI and UC Berkeley in that location, or gene name may be used to enter the system. The UCSC resources also allow sequence based searches via the BLAT server. BLAT tends to be a bit faster than NCBI Genome BLAST searches and quite a bit more convenient than the UCB sequence search tool (see below). The UCSC graphics are more primitive than either the UCB, NCBI or ENSEMBL viewers. Since all three viewers are playing from the same resources, what separates them is to a degree a user's personal preferences. The UCSC servers also allow convenient sequence downloads.

The UCSC BLAT server. BLAT is a an extremely fast sequence query system that will find regions similar to your uploaded or pasted query sequence. These next lines from the BLAT page offer a succinct description. "BLAT is not BLAST. DNA BLAT works by keeping an index of the entire Genome in memory. The index consists of all non-overlapping 11-mers except for those heavily involved in repeats. " There is a little bit of help on-line for BLAT.

The UCSC Genome Browser Help Adding and displaying your own annotations to the Genome browser is one VERY nice feature of the UCSC Genome Browser that's not available from NCBI. You will have to absorb a number of distinct syntax conventions however to make use of your own annotations.

The UCSC Table Browser Help

The UCSC Genome Bioinformatics Home Page.

Page 1 of 13Web Bioinformatics

11/5/2003http://people.musc.edu/~hazards/WebBioInformatics/UCSCGenomeViewer.htm

A worked Example Here's the basic Genome browser window showing the Genome, position and pixel width selection menus.



Here's the result obtained from typing in the gene name "casp7" for the human Genome. Zoom functions are at the top. Detail buttons are on the left and additional



display options may be selected from the bottom menus (mostly off-screen).



Below is a full view of the available option menus.

Here is the local genescape around CASP7. This is the result of a 10x zoom.



You should experiment with adding and removing various data panels from the display to get a feel for what is possible.



Here is the BLAT page:



And Here is the Genome Browser Page which resulted from a BLAT query with a human CASP7 cDNA query.



The UCSC Table Browser can retrieve data by a variety of criteria. Here is a the table set up page



Here is a result where the criterion was protein homology and the query CASP7. Note the expression pattern block on the left.



Here is the same search sorted by Gene Ontology GO value. Tne Gene Ontology entry for CASPASE 7 is at this link. The GO project is developing a set of vocabulary terms which describe in unambiguous terms what a gene product does in a suitable biological context. In this regard GO is functioning for genes rather like the EC number/nomenclature for enzymes. The goal of the GO project is to provide a concise, precise description of function.



By clicking on any of the table entries you connect to the UCSC summary page for that gene. Plan to spend about 15 minutes looking through this next link to the CASP7



summary. Look as well at the GeneCards Summary page for CASP7 (link near the top of the UCSC summary). The notion of function has high utility but you might ask yourself as you look through this collection, ' what does casp 7 really do?' . It is an enzyme, it is not expressed everywhere at all times. Examine the KEGG link and the BioCarta links in the Biochemical and Signaling Pathways section for some elegant graphical summaries of CASP7 function. CASP7 summary page. Here's the NCBI LocusLink page for CASP7. Here's another link to the GeneCards entry for CASP7. Here's the KEGG link. Here's a BioCarta Link. So with all this wealth of information about CASP7, what does CASP7 do? In YOUR OWN words!!!!!!!!!!!!

Sample Questions/Data

Look up "slc22a6"

Look up "abcg8"

Look up your favorite gene/protein.

Created by ESH 8-18-2003; updated 11-5-2003 11:30

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