SEQUENCE RETRIEVAL SYSTEM SEQUENCE RETRIEVAL SYSTEM SRS SRS Ashwin Sivakumar, 02/12/03 Ashwin...

SEQUENCE RETRIEVAL SYSTEMSEQUENCE RETRIEVAL SYSTEM

SRSSRS

Ashwin Sivakumar, 02/12/03Ashwin Sivakumar, 02/12/03

Hands on Workshop on Protein Analysis (HOW)Hands on Workshop on Protein Analysis (HOW)

http://srs.ebi.ac.ukhttp://srs.ebi.ac.uk

Temporary session

Permanentsession

DatabaseInformation-which are present-when indexed

Documentation

List of public servers

What is SRS?What is SRS?

Central resource for Central resource for molecular molecular biology databiology dataData retrieval systemData retrieval system- more than 250 databanks have been indexed. - more than 250 databanks have been indexed.

More than 35 SRS servers over the WWWMore than 35 SRS servers over the WWW

Data analysis applications serverData analysis applications server - 11 protein applications- 11 protein applications - 6 nucleic acid applications- 6 nucleic acid applications

- Uniform query interface on the webUniform query interface on the web

Data Jungle

Structural biology

molecularbiology

genetics

medicine

Sequencinginformation

physiologytoxicology

geneexpression

History of SRSHistory of SRS

1990 - Main author Dr. Thure Etzold1990 - Main author Dr. Thure Etzold– Development started in EMBL, HeidelbergDevelopment started in EMBL, Heidelberg

19971997– Moved to EBI in Cambridge. Development Moved to EBI in Cambridge. Development

work was supported by various grants work was supported by various grants amongst others from the EMBnet.amongst others from the EMBnet.

19981998– Etzold and his group join LionBiosciencesEtzold and his group join LionBiosciences

Why SRS?Why SRS?

Information retrievalInformation retrieval– Easy way to retrieve information from Easy way to retrieve information from

sequence and sequence-related databasessequence and sequence-related databases– Possibility to search for multiple words/other Possibility to search for multiple words/other

criteriacriteria

Linkage between different databasesLinkage between different databases– E.g. Find all primary structures with known E.g. Find all primary structures with known

three-dimensional structurethree-dimensional structure

... and much more... and much more

Philosophy of SRSPhilosophy of SRSOriginal database file -plain text, html, xml

Data Retrieval Searchable links between database entries

Index file

parsed

Temporary ProjectsTemporary ProjectsQueries and views are stored by the project Queries and views are stored by the project manager temporarilymanager temporarilyTemporary sessions last 24 hoursTemporary sessions last 24 hoursUseful when you:Useful when you:– Do not need to keep your resultsDo not need to keep your results– look something up quicklylook something up quickly– Run an occasional applicationRun an occasional application

Click on ‘Start’ paw on SRS start pageClick on ‘Start’ paw on SRS start page

Permanent ProjectsPermanent ProjectsQueries and views are stored by the project manager Queries and views are stored by the project manager in a single locationin a single locationThey are available for use in the futureThey are available for use in the futureUseful when:Useful when:– You want to return to a sessionYou want to return to a session– Want to have many projects in the same sessionWant to have many projects in the same session

Begin by clicking ‘Permanent session’ paw on SRS Begin by clicking ‘Permanent session’ paw on SRS start pagestart page– Just need to enter an SRS user name and re-enter Just need to enter an SRS user name and re-enter

this to return to same session again laterthis to return to same session again later

Workbenches

Query Forms

Library groups

Libraries

The Library Select Page

SRS main toolbar tabsSRS main toolbar tabs

Top PageTop Page: displays databases in different database : displays databases in different database groupsgroupsQueryQuery: displays either the standard or extended : displays either the standard or extended query formquery formResultsResults or “the query manager”:or “the query manager”: maintains a maintains a history of all the results obtained during a sessionhistory of all the results obtained during a sessionProjects or “the project manager”:Projects or “the project manager”: maintains a maintains a history of all queries and views used during a sessionhistory of all queries and views used during a sessionViews:Views: allows a user to define a user specific view allows a user to define a user specific view for one or more databasesfor one or more databasesDatabanks:Databanks: contains a list and some facts about the contains a list and some facts about the databases available in the systemdatabases available in the system

Search terms in SRSSearch terms in SRSSRS indexed fields can be searched using any of the SRS indexed fields can be searched using any of the following:following:– Single word searchSingle word search– Multiple word phrasesMultiple word phrases– Numbers and datesNumbers and dates– Regular expressionsRegular expressions– WildcardsWildcards

Search methodsSearch methodsQuick search button:Quick search button:– Works by searching all datafields of type text Works by searching all datafields of type text – The quickest way to generate query resultsThe quickest way to generate query results– For very general/broad searchesFor very general/broad searches

Example: get all mouse and mouse related proteins in Example: get all mouse and mouse related proteins in SWISS-PROTSWISS-PROT

All Entries button:All Entries button:– Returns all entries in the database selectedReturns all entries in the database selected

Search formsSearch forms : allow you to specify your area of interest in : allow you to specify your area of interest in more detailmore detail– Standard query formStandard query form– Extended query formExtended query form

Standard query formStandard query formEnter up to 4 separate search terms against up to 4 Enter up to 4 separate search terms against up to 4 datafields simultaneouslydatafields simultaneouslyCombine entries with logical operators ( and & or | Combine entries with logical operators ( and & or | butnot ! )butnot ! )Choose the number of entries to display per pageChoose the number of entries to display per pageRetrieve entries of type (entry or subentry(name))Retrieve entries of type (entry or subentry(name))Choose a view Choose a view – use an SRS predefined viewuse an SRS predefined view– create one of your own by selecting specific fields from a create one of your own by selecting specific fields from a

dropdown menu (and choose whether to view a list or table dropdown menu (and choose whether to view a list or table in SRS7)in SRS7)

QueryFields

Predefined views

User defined views

The Standard Query Page

Extended query formExtended query formCan enter search terms for as many fields as you wantCan enter search terms for as many fields as you wantCombine searches with logical operators ( and & or | butnot ! )Combine searches with logical operators ( and & or | butnot ! )Choose how many results to display per pageChoose how many results to display per pageChoose view and sequence format to useChoose view and sequence format to use– Can choose an SRS predefined viewCan choose an SRS predefined view– Define your own view by clicking the boxes next to the fields Define your own view by clicking the boxes next to the fields

that you want to have displayed (list or table option in SRS7)that you want to have displayed (list or table option in SRS7)Each field name has a hyperlink to the description page for that fieldEach field name has a hyperlink to the description page for that fieldForm provides less than ‘<‘ and greater than ‘>’ for numerical fieldsForm provides less than ‘<‘ and greater than ‘>’ for numerical fieldsChoose what type of entries to retrieve (entry, subentry (name))Choose what type of entries to retrieve (entry, subentry (name))– – on extended form if you query a subentry field, it defaults to on extended form if you query a subentry field, it defaults to

returning results of type subentry returning results of type subentry

Extended query page

Fields

Predefind views

User definedview

Differences in these 2 formsDifferences in these 2 formsRanges Ranges – standard must use ‘:’standard must use ‘:’– extended provides ‘<‘ and ‘>’extended provides ‘<‘ and ‘>’

Type retrievalType retrieval – standard defaults to retrieving entries of type ‘entry’standard defaults to retrieving entries of type ‘entry’– extended defaults to retrieving entries of type entry unless extended defaults to retrieving entries of type entry unless

you query a subentry field in which case the default is the you query a subentry field in which case the default is the subentry typesubentry type

Controlled vocabulary fieldsControlled vocabulary fields – standard does not provide you with a list for these fieldsstandard does not provide you with a list for these fields– extended provides a drop down menu for these fields extended provides a drop down menu for these fields

allowing you to select an optionallowing you to select an option

WildcardsWildcardsThese are useful when: These are useful when: – Searching for a group of words (eg. Words starting ‘cell’ and Searching for a group of words (eg. Words starting ‘cell’ and

ending ‘ase’ : cell*ase)ending ‘ase’ : cell*ase)– If unclear about how a word is spelt in a databaseIf unclear about how a word is spelt in a database

Two types:Two types:– * one or more characters of any value* one or more characters of any value– ? Single character of any value? Single character of any value

Any number of wildcards can be placed anywhere in a search Any number of wildcards can be placed anywhere in a search wordword

Placing a wildcard at the start of a word or string may increase Placing a wildcard at the start of a word or string may increase response time because all words in the index have to be response time because all words in the index have to be checked against the stringchecked against the string

Regular expressionsRegular expressionsNB: Must appear within forward slashes (/)NB: Must appear within forward slashes (/)Some operators:Some operators: ^ marks the start of a string /^glu/ begins with ‘glu’^ marks the start of a string /^glu/ begins with ‘glu’$ marks the end of a string /ase$/ ends with ‘ase’$ marks the end of a string /ase$/ ends with ‘ase’. dot is any single character. dot is any single character[…] characters in square brackets are regarded as a set, any of […] characters in square brackets are regarded as a set, any of

which can be matchedwhich can be matched[0-9] specifies a range of 1 to 9[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 zero or more times+ the preceding group may be repeated one or more times+ the preceding group may be repeated one or more times? The preceding character/group occurs one or zero times? The preceding character/group occurs one or zero times

Some examplesSome examples/^glu/ will find terms beginning with ‘glu’/^glu/ will find terms beginning with ‘glu’

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

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

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

then any number of characters and ending with ‘t’then any number of characters and ending with ‘t’

/sm[iy]th/ will find the words ‘smith’ or ‘smyth’/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/rho[1-9]/ will find the word ‘rho’ followed by a number from 1-9

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

NB. The ‘*’ symbol has two meanings:NB. The ‘*’ symbol has two meanings:

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

repeated zero or more timesrepeated zero or more times

- outside forward slashes it means any character- outside forward slashes it means any character

Numerical rangesNumerical rangesIn a numerical index it is possible to search numerical rangesIn a numerical index it is possible to search numerical ranges

- sequence lengths, mol. weights, dates….- sequence lengths, mol. weights, dates…. the ‘:’ is used for specifying ranges and ‘!’ for excluding valuesthe ‘:’ is used for specifying ranges and ‘!’ for excluding values– 400:500 all seq. with length between 400 and 500400:500 all seq. with length between 400 and 500– 400: all seq. with lengths greater than 400400: all seq. with lengths greater than 400– :500 all seq. with lengths less than 500:500 all seq. with lengths less than 500– 400:!500 all seq. with lengths bet. 400 and 500 excluding 500 400:!500 all seq. with lengths bet. 400 and 500 excluding 500

Can combine ranges using logical operatorsCan combine ranges using logical operators– 300:!400 | !500:600 or 300:600 ! 400:500300:!400 | !500:600 or 300:600 ! 400:500

Dates in SRS have 2 formats:Dates in SRS have 2 formats:– YYYYMMDD YYYYMMDD 2002120520021205– DD-MMM-YYYY DD-MMM-YYYY 05-Dec-2002 05-Dec-2002

Some examplesSome examples– Find entries with sequences having length betwwen 300 and Find entries with sequences having length betwwen 300 and

400 400 excluding 400 and between 500 and 600 excluding 500:excluding 400 and between 500 and 600 excluding 500: 300:!400 | !500:600 or 300:600 ! 400:500300:!400 | !500:600 or 300:600 ! 400:500

– Find entries that were created in the first half of 2001:Find entries that were created in the first half of 2001:01-jan-2001:30-jun-2001 or 20010101:20010630 01-jan-2001:30-jun-2001 or 20010101:20010630

– Find all entries updated since May this year:Find all entries updated since May this year:01-may-2002: or 20020501:01-may-2002: or 20020501:

SRS IndexingSRS IndexingSRS indexes database records using a ‘SRS indexes database records using a ‘word word by word’by word’ approach. approach.- DE Human glutathione transferase- DE Human glutathione transferase- The SRS description index will contain terms The SRS description index will contain terms

‘human’, ‘glutathione’ and ‘transferase’.‘human’, ‘glutathione’ and ‘transferase’.

(&) AND : (&) AND : ‘human ‘human && glutathione glutathione && transferase’ transferase’

(|) OR(|) OR :: ‘human ‘human || glutathione glutathione || transferase’ transferase’

(!) BUTNOT :(!) BUTNOT : ‘human ‘human !! glutathione glutathione !! transferase’ transferase’

EMBL

HUMANglutathione

transferase

human & glutathione & transferase

human & transferase ! glutathione gluthathione & transferase ! human

Databanks information pageDatabanks information pageLists the databases available in the system and a Lists the databases available in the system and a summary about them:summary about them:– Number of entries in the databaseNumber of entries in the database– Date it was indexedDate it was indexed– Group it belongs toGroup it belongs to– Its availability statusIts availability status

Hyperlinks to information page specific to each Hyperlinks to information page specific to each databasedatabase

Databanks Information Page

Database information pageDatabase information pageProvides a detailed description about the database contents, source, ftp site, Provides a detailed description about the database contents, source, ftp site, literature…literature…Lists information about the fields that are present in the database including:Lists information about the fields that are present in the database including:– Name of fieldName of field– Short name for fieldShort name for field– Type of field Type of field

index : it is indexedindex : it is indexednum : indexed and a numerical fieldnum : indexed and a numerical fieldid: unique fieldid: unique fieldshow: not indexed, just for displayshow: not indexed, just for display

– Number of keys for that fieldNumber of keys for that field– Date it was indexed Date it was indexed

Lists databases that it is linked to and how many entries are linked Lists databases that it is linked to and how many entries are linked respectivelyrespectively

PROSITE information page

Browsing indicesBrowsing indicesThis gives information on what is being indexed for a This gives information on what is being indexed for a particular fieldparticular field– Single words, multiple words, controlled vocabulary…..Single words, multiple words, controlled vocabulary…..

To browse an index go to the information page for a To browse an index go to the information page for a particular field from a certain databaseparticular field from a certain database– If you want to look at all indexed terms use ‘*’If you want to look at all indexed terms use ‘*’– If you want all terms beginning with trans use ‘trans*’ If you want all terms beginning with trans use ‘trans*’ – If you want all terms containing the string trans use ‘*trans*’If you want all terms containing the string trans use ‘*trans*’

Browsing the description field index for terms beginning with ‘trans’……...

Query managerQuery managerFound under the results tabFound under the results tab

Saves a history of results obtained in the sessionSaves a history of results obtained in the session

Page allows you to return to previous results and:Page allows you to return to previous results and:– Combine them using logical operators – thus Combine them using logical operators – thus

allowing you to perform a multi-step queryallowing you to perform a multi-step query– Use a different view to display themUse a different view to display them– Perform further actions link, save, deletePerform further actions link, save, delete

The Query Manager

My Queries

Combine

Operators

Project managerProject managerFound under the projects tabFound under the projects tab

Saves a history of queries performed in the sessionSaves a history of queries performed in the session

Can upload/download SRS session files from a Can upload/download SRS session files from a desktopdesktop

In a permanent session, the project manager can In a permanent session, the project manager can also:also:– Manage numerous SRS projects at the same timeManage numerous SRS projects at the same time– Move queries/views between projectsMove queries/views between projects– Upload/download projects to desktopUpload/download projects to desktop– Delete projectsDelete projects

Project manager page

User owned databanksUser owned databanks

Found in the category ‘user owned databanks’ on top Found in the category ‘user owned databanks’ on top pagepageUser can upload their own nucleotide or protein User can upload their own nucleotide or protein sequence data into a user owned databasesequence data into a user owned database– sequences must be in fasta formatsequences must be in fasta format– any number of sequences can be uploadedany number of sequences can be uploaded– database is specific to the individual and to the database is specific to the individual and to the

sessionsessionCan launch applications on database sequencesCan launch applications on database sequences

User owned dataUser owned data

•Paste or upload a file•Fasta formatted files•Any number of sequences•Maintained throughout user session

Operations on resultsOperations on results

Linking Linking : link results to other databases: link results to other databases

SavingSaving: save results in different formats to the : save results in different formats to the browser or a filebrowser or a file

ViewingViewing: view results using different formats: view results using different formats

Sequence analysisSequence analysis: launch applications on the : launch applications on the

resultsresults SRS6 – 11 protein applications, 6 nucleic acid SRS6 – 11 protein applications, 6 nucleic acid apps.apps.

SRS7 – more than 100 applications availableSRS7 – more than 100 applications available

The Results Page

Operations

SRS6 versus SRS7SRS6 versus SRS7SRS7 provides over 100 applications while SRS6 provides 17SRS7 provides over 100 applications while SRS6 provides 17

You can retrieve results in either list or table format in SRS7You can retrieve results in either list or table format in SRS7

In SRS6 only the table format is availableIn SRS6 only the table format is available

Current EBI version 7.1.1Current EBI version 7.1.1

SRS6 -- first viewSRS6 -- first view

Start a new session by clicking here.

Top pageTop page

1. Select one or more databases by ticking the corresponding box

2. Select type of query form

Different types of database in Different types of database in SRSSRS

Sequence & structureSequence & structure– DNA, protein, three-dimensional structuresDNA, protein, three-dimensional structures

Sequence-relatedSequence-relatedGene-relatedGene-related– Genome, mapping, mutations, transcription Genome, mapping, mutations, transcription

factorsfactors– SNPSNP

BibliographicBibliographic– Medline, enzymeMedline, enzyme

User-definedUser-defined

Standard query formStandard query form

1. Type text to search for

3. Select AND or OR if multiple search items are used

4. Select number of results to show at a time

2. Select field to search

5. Submit query

Query result -- table modeQuery result -- table mode5. Link sequences to

other databases

2. Accession number, description and sequence length

4. Mode of viewing can be changed

6. Possibility to analyse sequences with other tools, e.g. FastA and ClustalW

1. Hypertext links

3. Tick boxes to select/deselect sequences for further analyses

Example query Example query

Use SRS to answer the following question:Use SRS to answer the following question:For which short-chain dehydrogenases/ For which short-chain dehydrogenases/ reductases (SDR) are the three-reductases (SDR) are the three-dimensional structure known in PDB?dimensional structure known in PDB?

Example, Query formExample, Query form

1. Enter the search term ”sdr”

2. Enter in which field to search

Example, Query resultExample, Query result

Press the button Link in order to get to the Link page

Link pageLink page

1. You can link in three different ways

2. In this case, we select to link to PDB

3. The we select chunk size and view mode

4. Finally, we press the ”Submit link” button

Link resultsLink results

Example of a Swissprot entryExample of a Swissprot entry

Example of a Swissprot entry, Example of a Swissprot entry, cont.cont.

Click this link to get to the corresponding Medline entry (in PubMed)

PubMed entryPubMed entry

By clicking this link, you have the possibility to download the electronic version of the article.

The Top page tabThe Top page tab

The Query tabThe Query tab

The Results tabThe Results tab

The Sessions tabThe Sessions tab

The Views tabThe Views tab

The Databanks tabThe Databanks tab

AcknowledgementsAcknowledgements

¤ Bengt Persson¤ Bengt Persson MBB, Karolinska institutet (demos)MBB, Karolinska institutet (demos)

¤ 2can tutorial on SRS at EBI¤ 2can tutorial on SRS at EBI

http://downloads.lionbio.co.uk/publihttp://downloads.lionbio.co.uk/publicsrs.htmlcsrs.html (The latest SRS server list) (The latest SRS server list)

server breakupserver breakup

srs.sanger.ac.uk (5)srs.sanger.ac.uk (5)

srs.ebi.ac.uk (5)srs.ebi.ac.uk (5)

srs.csc.fi (5)srs.csc.fi (5)

titanic.thep.lu.setitanic.thep.lu.se/srs71//srs71/ (5) (5)

If you think the load on a server is slowing If you think the load on a server is slowing your query, chose an alternative server to your query, chose an alternative server to practice on.practice on.