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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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SEQUENCE RETRIEVAL SYSTEM SRS

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Sequence retrieval system srs l.jpg

SEQUENCE RETRIEVAL SYSTEM SRS

Tuomas Hätinen


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Motivation

Sequencing

information

genetics

Structural

biology

molecularbiology

medicine

physiology

toxicology

gene

expression


Motivation l.jpg

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


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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 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.


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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’

/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


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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’ : 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


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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


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