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SEQUENCE RETRIEVAL SYSTEM SRS. Tuomas Hätinen. Motivation. Sequencing information. genetics. S tructural biology. molecular biology. medicine. physiology. toxicology. gene expression. Motivation. There are 3 main sequence retrieval systems: SRS (highly recommended)

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slide2

Motivation

Sequencing

information

genetics

Structural

biology

molecularbiology

medicine

physiology

toxicology

gene

expression

motivation
Motivation
  • There are 3 main sequence retrieval systems:
    • SRS (highly recommended)
    • Entrez (easier to use but more limited)
    • DBGet (less recommended)
  • This is a workshop on using SRS
  • Start one of the servers below:
    • http://srs.ebi.ac.uk
    • http://csc-fserve.hh.med.ic.ac.uk/srs71
    • http://walnut.bioc.columbia.edu/srs7/
    • http://emb2.bcc.univie.ac.at:8080/srs/
    • http://oryx.ulb.ac.be:8080/srs

Full list of srs servers available from:

http://downloads.lionbio.co.uk/publicsrs.html

what is srs introduction
What is SRS?: Introduction
  • Central resource for molecular biology data
  • Data retrieval system

- more than 250 databanks have been indexed. More than 35 SRS servers over the WWW

  • Data analysis applications server

- 11 protein applications

- 6 nucleic acid applications

  • Uniform query interface on the web
what is srs history
What is SRS?: History
  • 1990 - Main author Dr. Thure Etzold
    • Development started in EMBL, Heidelberg
  • 1997
    • Moved to EBI in Cambridge. Development work was supported by various grants amongst others from the EMBnet.
  • 1998
    • Etzold and his group join LionBiosciences
why srs
Why SRS?
  • Information retrieval
    • Easy way to retrieve information from sequence and sequence-related databases
    • Possibility to search for multiple words/other criteria
  • Linkage between different databases
    • E.g. Find all primary structures with known three-dimensional structure
  • ... and much more
comments
Comments
  • SRS is both a simple and complicated tool with a number of features.
  • Can take a few days to get accustomed to.
  • We will run through some important features during the lecture.
  • We will apply these features as well as other new ones in the practical session.
what can you do in srs that you can t do in uniprot
What can you do in SRS that you can’t do in UniProt
  • Sophisticated searches: eg wildcard searches, regexp searches
  • SRS consolidates multiple databases.
  • Many tools are available in SRS
  • Saving of projects
  • Why bother with Uniprot? Speed.
temporary projects
Temporary Projects
  • Queries and views are stored by the project manager temporarily
  • Temporary sessions last 24 hours
  • Useful when you:
    • Do not need to keep your results
    • look something up quickly
    • Run an occasional application
  • Click on ‘Start’ paw on SRS start page
some examples
Some examples

/^glu/ will find terms beginning with ‘glu’

/ase$/ will find terms ending with ‘ase’

/c.t/ will find the words cat, cot, cut…….

/c.*t/ will find terms beginning with ‘c’ and

then any number of characters and ending with ‘t’

/sm[iy]th/ will find the words ‘smith’ or ‘smyth’

/rho[1-9]/ will find the word ‘rho’ followed by a number from 1-9

/mue?ller/ will find ‘muller’ or ‘mueller’

NB. The ‘*’ symbol has two meanings:

-within forward slashes ‘/’ it means the preceding group may be

repeated zero or more times

- outside forward slashes it means any character

srs query syntax
SRS Query syntax
  • SRS indexes database records using a ‘word by word’ approach.

- DE Human glutathione transferase

    • The SRS description index will contain terms ‘human’, ‘glutathione’ and ‘transferase’.
boolean operators
Boolean operators
  • (&) AND : ‘human & glutathione & transferase’
  • (|) OR: ‘human | glutathione | transferase’
  • (!) BUTNOT : ‘human ! glutathione ! transferase’
wildcards
Wildcards
  • These are useful when:
    • Searching for a group of words (eg. Words starting ‘cell’ and ending ‘ase’ : cell*ase)
    • If unclear about how a word is spelt in a database
  • Two types:
    • * one or more characters of any value
    • ? Single character of any value
  • Any number of wildcards can be placed anywhere in a search word
  • Placing a wildcard at the start of a word or string may increase response time because all words in the index have to be checked against the string
srs regular expressions
SRS Regular expressions
  • NB: Must appear within forward slashes (/)
  • Some operators:

^ marks the start of a string /^glu/ begins with ‘glu’

$ marks the end of a string /ase$/ ends with ‘ase’

. dot is any single character

[…] characters in square brackets are regarded as a set, any of which can be matched

[0-9] specifies a range of 1 to 9

* the preceding group may be repeated zero or more times

+ the preceding group may be repeated one or more times

? The preceding character/group occurs one or zero times

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