Introduction to SRS

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Introduction to SRS

Frankie Cheung [email protected]

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Introduction to SRS

Part 0. IntroductionPart 0. Introduction

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SRS IntroductionSRS system started out as

a Sequence Retrieval Sequence Retrieval SystemSystem that employed sophisticated parsing and parsing and indexingindexing of database text files

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SRS IntroductionFast access Fast access to diverse life science data - ge

netic, protein, cellular, molecular, and clinical - for researchers and bioinformaticians

Integration of public and proprietary data through

one interfaceone interface Unique ability to perform cross-database cross-database

queriesqueries Rapid string searchRapid string search of large volumes of

data Seemless integration of data and anintegration of data and an

alysis tools alysis tools

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Starting SRS Browse the BIOSUPPORT Hompage:

http://bioinfo.hku.hk/ Select “Tools”“Tools” Option

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Starting SRS At the “Tools” page, find and click on the

Sequence Retrieval System Sequence Retrieval System (SRS)(SRS) system

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SRS Main Page After successful login, the default page is a

“Temporary ProjectTemporary Project”.

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SRS Main Page For a “Temporary ProjectTemporary Project”, the result of

your work would not be stored after you close SRS.

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SRS Main Page

Starting a “Permanent ProjectPermanent Project”, the result of your work would be stored even after you close SRS.

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Permanent Project After selecting a “Permanent ProjectPermanent Project”,

your account name and project name will be displayed. (Since no password protection under current policy, this approach is not recommended.)

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Permanent Project All the query and job result will be saved in

your “Permanent ProjectPermanent Project”.

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Permanent Project Option “Save to desktopSave to desktop” : download & save

your project info to your local machine

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Permanent Project Option “Rename projectRename project” : change the name

of your project

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Permanent Project Option “Delete projectDelete project” : delete all the related

information of your current project

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“Quick Searches” page :

Quick access with default databank selection

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“Quick Text Search” Quick sequence query with default

databank selection Enter your search string and click “Search”

to start searching

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“Quick Text Search” Default Databank Setting:

Nucleotide Seq EMBL

Protein Seq SWALL

Protein Structure PDB

Genome LocusLink

Mutations OMIM

Metabolic Pathway Pathway

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Introduction to SRS

Part 1. Simple QueryPart 1. Simple Query

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Simple query Go back to “Select DatabankSelect Databank”, click

on “PIRPIR” to select “PIR” databank

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Simple query Then click the “QueryQuery” button to fill in the

query form

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Simple query Click the first “AllTextAllText” pull down menu to

change it to “DescriptionDescription” Enter “cytochromecytochrome” at the blank besides

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Simple query Click the second “AllTextAllText” pull down

menu to change it to “OrganismOrganism” Enter “pigpig” at the blank besides

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Simple query Click the “SearchSearch” button to start

searching any sequence in PIR databanks satisfy your query form

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Simple query After searching for awhile, there would be

some result listing entries. Try to click the PIR:S26019PIR:S26019 entry

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Gene Sequence SRS would display the PIR:S26019 descri

ption: including ID, accession numbeID, accession number, description, keywordsr, description, keywords, etc

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Gene Sequence Scroll down to see the reference related to

this sequence, there is also a Medline rMedline referenceeference hyperlink available

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Gene Sequence Scroll down to see the gene functiongene function a

nd the gene sequencegene sequence

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Gene Sequence Save the gene sequence information to your local

machine Click the “SaveSave” button at the leftmost panel

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Gene Sequence Click the “Output toOutput to” button to choose the

text/html format

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Gene Sequence Click the “Use View” button to choose the

“Complete entriesComplete entries” format

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Gene Sequence Then click “savesave” to save again the PIR:S26019

to your local machine

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Simple query: Exercise

15 Minutes Break15 Minutes Break

Please try the following exercises Please try the following exercises by yourself!by yourself!

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Question 1. Question 1.

Search all the “SARS virus” in ESearch all the “SARS virus” in EMBL databasesMBL databases

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Simple query: Exercise 1. Search all the “SARS virus” in EMBL dat

abases

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abases

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abases:

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How many CDS regions for the “How many CDS regions for the “EMBL:AY278488” (SARS coronaEMBL:AY278488” (SARS coronavirus BJ01) ?virus BJ01) ?

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Simple query: Exercise 2. Click to see the detail AY278488

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Simple query: Exercise 2. Count the number of CDS entries

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Simple query: Exercise 2. CDS entries of EMBL:AY278488

orf1ab orf1a polyprotein spike glycoprotein S putative uncharacterized protein 1 putative uncharacterized protein 2 envelope protein E membrane protein M putative uncharacterized protein 3 putative uncharacterized protein 4 nucleocapsid protein N putative uncharacterized protein 5

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What is the protein ID for EMBL:What is the protein ID for EMBL:AY278741 (SARS coronavirus UrAY278741 (SARS coronavirus Urbani) spike glycoprotein?bani) spike glycoprotein?

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Simple query: Exercise 3. EMBL:AY278741

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Following the link of the spike glyFollowing the link of the spike glycoprotein of EMBL:AY278741, wcoprotein of EMBL:AY278741, what is the biological function of thihat is the biological function of this spike-protein? s spike-protein?

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Simple query: Exercise 4. Find biological function of VGL2_CVHSA

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Simple query: Exercise 4. Find biological function of VGL2_CVHSA

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Introduction to SRS

Part 2. Extended SearchPart 2. Extended Search

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Extended Search Click the “Select DatabanksSelect Databanks” button at

the top to select PIR as query targe

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Extended Search Click the “QueryQuery” button at the top to back to

query form

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Extended Search Click the “Extended QueryExtended Query” button at the

left panel to display the extended search form

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Extended Search In the “ExtendedExtended” search form, find the

“Super FamilySuper Family” field and then enter

“cytochrome-ccytochrome-c ” Click the “SearchSearch” to start the query

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Extended Search After searching for awhile, there would be

extended search result list appear

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Using Search Results Click the “ResultResult” button at the top to reuse

your query result

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Using Search Results In the “Result” pages, enter “Q1 !Q3Q1 !Q3” at the

top blank field and click “Expression” to combine 2 queries results(Q1 but not Q3), click “Search”

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Using Search Results After waiting for awhile, SRS give the query result

of Query 1 but not Query 3 => Query of all sequences in PIR with description

having “cytochrome” string and organism having “pig”, but their super-family having no string of “cytochrome-c”

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Extended Search: Exercise



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Extended Search : Exercise


Search all the human DNA sequeSearch all the human DNA sequence entries created after 01-Jan-nce entries created after 01-Jan-2003 with sequence length great2003 with sequence length greater than 100000 in EMBL.er than 100000 in EMBL.

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Extended Search : ExerciseQuestion 1.

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Search all the mouse protein seqSearch all the mouse protein sequence entries created before 01-uence entries created before 01-Jul-2002 with NCBI TAX_ID less Jul-2002 with NCBI TAX_ID less than 4000 in SWISSPROT.than 4000 in SWISSPROT.

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Using the previous result, search Using the previous result, search the entries that have links to “PRthe entries that have links to “PROSITE” database.OSITE” database.

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Extended Search : ExerciseQuestion 3. Identify the Query ID (Q6 in this case,

you may not have same query ID)

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Extended Search : ExerciseQuestion 3. Enter the expression to find the entries

in previous that have link to “PROSITE” database (“Q6<PROSITE” in this case, you may not have same query ID)

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Extended Search : ExerciseQuestion 3. Result similar to this one

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Introduction to SRS

Part 3. Linking related Part 3. Linking related sequence / databasesequence / database

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Linking Related Sequence Go back to result #3, Click to select the first first

two sequencetwo sequence Click “LinkLink” button to search for the related

sequence

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Linking Related Sequence Ensure the choice “Find related entriesFind related entries” Click “EMBLEMBL” as to search related sequence in

this databank Click “SearchSearch” button

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Linking Related Sequence Result: 5 entries found in “EMBL” are the the

related sequence with your selected sequence

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Linking Related Sequence Refine the result list to “SeqSimpleView” in the left

panel

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Linking Related Sequence Result List

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Linking database: Exercise



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Question 1.Question 1.Find in the EMBL database the corFind in the EMBL database the cor

responding sequences that link tresponding sequences that link to the longest sequence of the preo the longest sequence of the previous result (question #2 in extenvious result (question #2 in extended search)ded search)

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Linking database : ExerciseQuestion 1. Go back to the previous result Question

#2 in extended search(Query #6 in this case)

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Linking database : ExerciseQuestion 1. Sort to find the longest sequence from

the result list

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Linking database : ExerciseQuestion 1. Sort to find the longest sequence from

the result list

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Linking database : ExerciseQuestion 1. Click the “Link” button after selecting the

longest sequence

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Linking database : ExerciseQuestion 1. Search the “EMBL” database which

have related entries links to selected sequence

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Linking database : ExerciseQuestion 1. EMBL:AP000423 is matched

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Question 2.Question 2.Using the previous result (question Using the previous result (question

#1 in simple query), make a quer#1 in simple query), make a query to find the entries which have liy to find the entries which have links to SWISSPROT databasenks to SWISSPROT database

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Linking database : ExerciseQuestion 2. Go back to the previous result Question

#1 in simple query (Query #2 in this case)

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Linking database : ExerciseQuestion 2. Click the “Link” button with “Unselected

only”

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Linking database : ExerciseQuestion 2. Select “Swissprot”, show only results wit

h related entries link to “Swissprot”

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Linking database : ExerciseQuestion 2. Around 11 EMBL entries are matchedReturn list should be EMBL entries but not

SWISSPROT entries

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Question 3.Question 3.Using the previous result (question Using the previous result (question

#1 in simple query), make a quer#1 in simple query), make a query to find the entries which have ny to find the entries which have no links to SWISSPROT databaseo links to SWISSPROT database

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Linking database : ExerciseQuestion 3. Select “Swissprot”, show only results wit

hout related entries

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Linking database : ExerciseQuestion 3. Around 32 EMBL entries are matched

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Introduction to SRS

Part 4. ApplicationPart 4. Application

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Application: BLAST Go back to the query result page -> Q9

"(([PIR-ID:ODHU1] | [PIR-ID:ODBO1]) > EMBL )" Click the checkbox of EMBL:MIHSM1 and then click

“Launch” with application “BLASTBLASTNN”

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Application: BLAST BLAST window appear and change the “Complete

Database to search” to Yeast Complete GeYeast Complete Genomenome

Change other parameters as you like and then click “Launch” to execute

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Application: BLAST

BLAST job was submitted to the batch queue

Click the hourglass icon (left top corner) to check whether the job is finished?

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Application: BLAST

After the job result is ready, click to see the BLAST job result

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Application: BLAST

After waiting for awhile, the BLAST result list appear, click any one of them to view the detail

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Application: BLAST

BLAST alignment result with the databanks

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Application: Clustalw

Go back to blast result list. Then click the checkbox to select first 5 sequence

Click the Application pull down menu to “NCNClustalWlustalW”

and then click “LaunchLaunch”

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Then “ClustalW” window appear and change the parameters as you like

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After click “LaunchLaunch”, SRS would launch clustalw with you selected sequence and give the result

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Application: EMBOSS(eg: PRETTYPLOT)

Using the ClustalW result, and then click “Tools”

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Choose “prettyplotN” , and then click “Launch”

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It jump to “prettyplotN” interface, scroll down …..

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Click to select “Display the consensus”, and then click “Launch”

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Click the first graphic file to view the result, while the second file would be empty

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You will see the identical residue shown in RED color The last line show the consensus of the alignment

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Application: EMBOSS(eg: SIXPACK)

Go back to the query result page -> Q9

"(([PIR-ID:ODHU1] | [PIR-ID:ODBO1]) > EMBL )" Click the checkbox of EMBL:MIHSM1 and then click “Tools”

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Choose “SIXPACK” and then click “Launch”

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click “Launch” to run SIXPACK program

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At the result page, see the number of possible ORF in 6-frame

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See the translation in all 6-frames

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Application: EMBOSS(eg: TMAP)

Several EMBOSS can be directly launched by SRS: for example, TMAP

Go back to Q4 result and click the checkbox of PIR:S26019 and then click “Tools”

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It will jump to show a list of application, change the pull-down menu to “TMAPTMAP” and click launch

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“TMAP” window appear and click “Launch” to execute TMAP with your selected sequence

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After waiting for awhile, “TMAP”give out the predicts transmembrane segments result

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Scroll at the bottom to click to see the membrane spanning regions diagram

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Application : Exercise



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Application: Exercise

Question 1.Question 1.Do the sequence alignment of the Do the sequence alignment of the

5 shortest sequence from the pre5 shortest sequence from the previous result (question #2 in extenvious result (question #2 in extended search) using clustalwded search) using clustalw

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Application: ExerciseQuestion 1. Go back to the previous result Question

#2 in extended search, Q6 in this case

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Application: ExerciseQuestion 1. Sort to find the 5 shortest sequences

from the result list

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Application: ExerciseQuestion 1. Launch “Clustalw” after selecting 5 short

est sequences

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Application: ExerciseQuestion 1. No need to modify any parameters, click

“launch” to start sequence alignment

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Application: ExerciseQuestion 1.

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Question 2.Question 2.Do the BLAST search using the EDo the BLAST search using the E

MBL:AY278491 (HKU-SARS viruMBL:AY278491 (HKU-SARS virus) sequence against EMBL (Reles) sequence against EMBL (Release): VRL(virus) databasease): VRL(virus) database

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Application: ExerciseQuestion 2. Go back to previous result list(Q2 in

normal case) to find the HKU-SARS virus

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Application: ExerciseQuestion 2. Search against the Viruses database

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Application: ExerciseQuestion 2. After waiting for few minutes, BLAST

result list display

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Application: ExerciseQuestion 2. See the BLAST result vs TOR2

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Question 3.Question 3.Find the transmembrance segmentFind the transmembrance segment

s of the SWISSPROT:VME1_CVs of the SWISSPROT:VME1_CVHSA (SARS virus M-protein) seqHSA (SARS virus M-protein) sequence using TMAPuence using TMAP

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Application: ExerciseQuestion 3. After finding the sequence, launch “tmap

”

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Application: ExerciseQuestion 3. After finding the sequence, launch “tmap

”

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Introduction to SRS

Part 5. OthersPart 5. Others

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User submit own sequence:

User can submit their own sequence to work with SRS

Go to “Select Databanks”, click to “Expand all” and find the “User Owned Databanks”

Click the “Add Data” beside USERDNA

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Enter your own DNA sequence in the blank field Then click “Launch” to input your own sequence t

o the UserDNA databank

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Wait for SRS to store your input DNA sequence

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Your sequence has been successfully input to the USERDNA databank

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Then you can search related link sequence or launch application with your sequence

For example, you can launch BLAST with your input sequence

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SRS On-Line Help

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SRS On-Line Help

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Documents

Introduction to SRS