Querying - SRS Quick Search

   

SRS Quick Search & the SRS Start Page

   
  These pages are virtually identical, with the exception that the SRS Start page includes the option to start a permanent project, whereas the SRS Quick Search page tells you information about your current session.

Use the Quick Search or Start pages to:

  • Perform one of several quick searches.
  • Launch analysis tools.
  • Access information about the available databases.
  • Access the on-line documentation.
  • Start a permanent project (when SRS Start page only).
Typical Quick Searches include:

  • Quick Text Search.
  • Sequence Similarity / Homology Search.
These searches are particularly useful to those who use SRS infrequently, or just want to do a quick search without needing to understand how to use SRS in detail.

Main Tasks
FAQs
Use the Quick Text Search How do I search for more than one term?
Use the Sequence Similarity / Homology Search How do I get a suitable sequence to enter?
Launch analysis tools What is meant by more advanced searching?
Run a canned query How do I find out about the databanks?
Start a permanent project How do I get to the online documentation?
What is the difference between temporary and permanent projects?
When should I use temporary and permanent projects?

More about Quick Search.

See "Starting an SRS Project" in chapter 1, "SRS Quick Tour", of the SRS User Guide , and chapter 2, "SRS Projects" , of the SRS User Guide for how to use this page.

Quick Search - Tasks

   
 

Quick Text Search

  1. From the drop-down list, select the type of data for which you want to search (beside Get:).
  2. Type your search term(s) in the text box beside matching.
  3. Click the button within the Quick Text Search area.
More Examples:See an example of how to use this page.

Note:Unlike searches using the Standard Query Form or the Extended Query Form you do not have to select a databank before you search. Choosing the type of data automatically selects the appropriate databanks.

Sequence Similarity / Homology Search

  1. From the drop-down list, select the type of data for which you want to search (beside Get:).
  2. Enter your sequence in the sequence text box.
  3. Click the button within the Sequence Similarity / Homology Search area.
More Examples:See an example of how to use this page.

Tip:Copy and paste may be useful for entering sequence data.

Start a Permanent Project

To start a permanent project:

  1. Click the Start a Permanent Project link

 
Figure 3.1 Starting a permanent project.

    This takes you to the Select Databanks To Search page where you can begin working with SRS.
Note:You can only start a permanent project from the SRS Start page, the option does not appear on the SRS Quick Search page. Clicking on any of the other options on the Start page (including the Quick Searches) will perform the selected task within a temporary project.

Quick Search - Worked Examples

   
 

Quick Text Search - Worked Example

  1. Select Protein Sequence from the drop-down list (beside Get).
  2. Type kinase in the text box beside matching.
  3. Click the button within the Quick Text Search area. Your results will be displayed using the selected view.

Sequence Similarity / Homology Search - Worked Example

  1. Select Nucleotide Sequence from the drop-down list (beside Get).
  2. Copy the protein sequence data below (leaving out the header line, which starts with >) and paste it into the sequence text box.
>LACI_ECOLI P03023 LACTOSE OPERON REPRESSOR.
MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQ
SLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVS
GLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQ
QIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPT
AMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPSTTIKQDFRLLGQTS
VDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPRALADSLMQLARQVSRLESGQ
  1. Click the button within the Sequence Similarity / Homology Search area. Your results will be displayed using the default view.

Quick Search - FAQs

   
 

Searching For More Than One Term

If you want to search for more than one term, simply write in the terms you require, separated by the standard SRS "combine search" operators, & (AND), ! (BUTNOT), |(OR).

For example, to search for kinase and amylase, enter: kinase & amylase in the text box. To search for entries which contain glucose and amylase, but do not contain kinase, enter: (glucose & amylase) ! kinase.

Tip:SRS is case insensitive so it does not matter whether you use uppercase or lowercase letters, or a mixture.

Getting a Suitable Sequence

Your sequences might come from almost any data source, e.g. your own research, be sent to you by a fellow researcher (e.g. by email), from a book, from a previous SRS search, etc.

What is Meant by More Advanced Searching?

More advanced searches make use of the Standard Query Form and the Extended Query Form. These allow you to search using a much bigger range of criteria than is possible using the quick searches.

How Do I Find Out About the Databanks?

  1. Click on the Information tab.
  2. On the List of Databanks page you can see a list of which databanks are available, which groups they belong to, etc.
  3. Click on the link for an individual databank to find out more about it.

How Do I Get to the Online Documentation?

  1. Click on the Help Center link in the Tips box on the Start or SRS Quick Search pages:

 
Figure 3.2 Clicking on the Help Center link.

  1. On the SRS Documentation page, use the tabs to locate items of interest.
  2. If you want to look at Administrator documentation, click on the Admin Help tab to display the available guides.
Tip:You can get to the documentation from any SRS page by clicking the button at any time. This will take you directly to the documentation pages that are relevant to the SRS page you were using.

What is the Difference Between Temporary and Permanent Projects?

There are two types of project that can be used with SRS: temporary and permanent. These are described below.

When you use a temporary project, your queries and views are stored in a temporary location. They may remain available for a time after you have finished working, but you should not rely on this. If you bookmark the page in your web browser, you should be able to return to the project until the System Administrator clears the files.

Permanent projects are used within a permanent SRS user account. There may be one or more (up to 99) projects within any such account. All your queries and views are stored in a project or projects. The fact that the projects are part of a user account, means that they remain available for you to use in the future, whenever you choose to return to that user account. User accounts (and the permanent projects within them) can also be password protected, allowing you to restrict access.

When Should I Use Temporary and Permanent Projects?

You should use a temporary project for:

  • Simple searches. For example, a temporary project is useful if you want to look something up quickly, or run an occasional BLAST search.
To find out more about running a temporary project see "Temporary Projects" in chapter 2, "SRS Projects", of the SRS User Guide

You should work in a permanent project if any of the following apply:

  • You or a colleague will want to return to a project at a later time.
  • You want to be able to move your work from one project to another.
  • You want to keep a safe record of all your projects.
  • You want to recall any of your previous permanent or saved projects.
To find out more about running a permanent project see "Permanent Projects" in chapter 2, "SRS Projects", of the SRS User Guide

Quick Search - Reference

   

 
Figure 3.3 The SRS Quick Search page.

Getting to the Quick Search Page

This page can be reached by clicking the Quick Searches tab.

Information on Quick Search

Quick Text Search

This option enables you to perform a quick text search of a limited selection of databanks (typically EMBL or SWISSPROT) without the need to go through the Select Databanks to Search page and use a Query Form.

Get
This drop down list contains the options controlling which databanks are searched. For example choosing Nucleotide Sequences will search the EMBL databank. Choosing Protein Sequences will search the SWISS-PROT databank.

matching
The word or phrase for which you wish to search should be typed here.

Sequence Similarity / Homology Search

This search allows you to compare an existing sequence to others in the databank, looking for appropriate similarities. It makes use of the various BLAST analysis tools.

Get
This drop down list contains the options controlling which databanks are searched. For example choosing Nucleotide Sequences will search the EMBL databank. Choosing Protein Sequences will search the SWISS-PROT databank.

Sequence box
Enter your sequence into this text box. The sequence may come from any source, and the easiest way to add it to the sequence text box is often to use copy and paste.

Analysis Tools
Four different tools are used: BlastP, BlastX, TBlastX and TBlastP. The choice depends on the combination of sequence types used for the search. The table below shows which tool is used with which combination of sequence types:
Databank
EMBL (Nucleotide)
SWISS-PROT (Protein)
Input Nucleotide Sequence
 BlastN BlastX
Input Protein Sequence
 TBlastN BlastP

Starting SRS - Reference

   

 
Figure 3.4 SRS Start page.

Getting to the Start Page

This is the first page you will see when you start SRS.

Options

Figure 3.4 shows the options that are available on the Start page. Most of these options are identical to those on the SRS Quick Search page. This section describes only the options that are different.

Start a Permanent Project

This option allows you to start a permanent project (see "Permanent Projects" in chapter 2, "SRS Projects", of the SRS User Guide ). You will be asked to identify your account to the system either through a JavaScript prompt or by way of the web server authentication prompt. Your project will be part of an account, and it is the account name that is used to identify you, and access the projects within that account on subsequent occasions.

Clicking the Start a Permanent Project option will take you to the Project Manager page for permanent projects.

Other Information

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