SEQUENCE RETRIEVAL SYSTEM SRS

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SEQUENCE RETRIEVAL SYSTEM SRS

• Tuomas Hätinen

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Motivation
Sequencing information
genetics
Structural biology
molecularbiology
medicine
physiology
toxicology
gene expression
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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.at8080/srs/
• http//oryx.ulb.ac.be8080/srs
• Full list of srs servers available from
• http//downloads.lionbio.co.uk/publicsrs.html

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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

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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

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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

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Why SRS?
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SRS construction
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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.

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What can you do in SRS that you cant 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.

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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

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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
• /smiyth/ will find the words
  smith or smyth
• /rho1-9/ 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

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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.

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Boolean operators

• () AND human glutathione transferase
• () OR human glutathione transferase
• (!) BUTNOT human ! glutathione ! transferase

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Wildcards

• These are useful when
• Searching for a group of words (eg. Words
  starting cell and ending ase cellase)
• 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

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Regular expressions
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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