Introduction to SRS H K U Computer Centre

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Introduction to SRS H K U Computer Centre Frankie Cheung frankie@cc. hku. hk

Introduction to SRS H K U Computer Centre Frankie Cheung frankie@cc. hku. hk

Introduction to SRS H K U Computer Centre Part 0. Introduction

Introduction to SRS H K U Computer Centre Part 0. Introduction

H K U Computer Centre SRS Introduction |SRS system started out as a Sequence

H K U Computer Centre SRS Introduction |SRS system started out as a Sequence Retrieval System that employed sophisticated parsing and indexing of database text files

SRS Introduction | Fast access to diverse life science data - genetic, protein, cellular,

SRS Introduction | Fast access to diverse life science data - genetic, protein, cellular, molecular, and clinical for researchers and bioinformaticians | Integration of public and proprietary data through one interface | H K U Computer Centre Unique ability to perform cross-database queries | Rapid string search of large volumes of data | Seemless integration analysis tools of data and

Starting SRS | Browse the BIOSUPPORT Hompage: http: //bioinfo. hku. hk/ | Select “Tools”

Starting SRS | Browse the BIOSUPPORT Hompage: http: //bioinfo. hku. hk/ | Select “Tools” Option H K U Computer Centre

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

Starting SRS | At the “Tools” page, find and click on the Sequence Retrieval System (SRS) system H K U Computer Centre

SRS Main Page | After successful login, the “Temporary Project”. H K U Computer

SRS Main Page | After successful login, the “Temporary Project”. H K U Computer Centre default page is a

SRS Main Page | For a “Temporary Project”, Project the result of your work

SRS Main Page | For a “Temporary Project”, Project the result of your work would not be stored after you close SRS. H K U Computer Centre

SRS Main Page | H K U Computer Centre Starting a “Permanent Project”, the

SRS Main Page | H K U Computer Centre Starting a “Permanent Project”, the result of your work would be stored even after you close SRS.

Permanent Project selecting a “Permanent Project”, your account name and project name will be

Permanent Project selecting a “Permanent Project”, your account name and project name will be displayed. (Since no password protection under current policy, this approach is not recommended. ) | After H K U Computer Centre

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

Permanent Project | All the query and job result will be saved in your “Permanent Project”. H K U Computer Centre

Permanent Project Option | “Save to desktop” : download & save your project info

Permanent Project Option | “Save to desktop” : download & save your project info to your local machine H K U Computer Centre

Permanent Project Option | “Rename project” : change the name of your project H

Permanent Project Option | “Rename project” : change the name of your project H K U Computer Centre

Permanent Project Option | “Delete project” : delete all the related information of your

Permanent Project Option | “Delete project” : delete all the related information of your current project H K U Computer Centre

“Quick Searches” page : | Quick access with default databank selection H K U

“Quick Searches” page : | Quick access with default databank selection H K U Computer Centre

“Quick Text Search” | Quick sequence query with default databank selection | Enter your

“Quick Text Search” | Quick sequence query with default databank selection | Enter your search string and click “Search” to start searching H K U Computer Centre

“Quick Text Search” | Default Databank Setting: Nucleotide Seq EMBL Protein Seq SWALL H

“Quick Text Search” | Default Databank Setting: Nucleotide Seq EMBL Protein Seq SWALL H K U Computer Centre Protein Structure PDB Genome Locus. Link Mutations OMIM Metabolic Pathway

Introduction to SRS H K U Computer Centre Part 1. Simple Query

Introduction to SRS H K U Computer Centre Part 1. Simple Query

Simple query back to “Select Databank”, click on “PIR” to select “PIR” databank |

Simple query back to “Select Databank”, click on “PIR” to select “PIR” databank | Go H K U Computer Centre

Simple query click the “Query” button to fill in the query form | Then

Simple query click the “Query” button to fill in the query form | Then H K U Computer Centre

Simple query the first “All. Text” pull down menu to change it to “Description”

Simple query the first “All. Text” pull down menu to change it to “Description” | Click | Enter H K U Computer Centre “cytochrome” at the blank besides

Simple query the second “All. Text” pull down menu to change it to “Organism”

Simple query the second “All. Text” pull down menu to change it to “Organism” | Click | Enter H K U Computer Centre “pig” at the blank besides

Simple query the “Search” button to start searching any sequence in PIR databanks satisfy

Simple query the “Search” button to start searching any sequence in PIR databanks satisfy your query form | Click H K U Computer Centre

Simple query | After searching for awhile, there would be some result listing entries.

Simple query | After searching for awhile, there would be some result listing entries. | Try to click the PIR: S 26019 entry H K U Computer Centre

Gene Sequence | SRS would display the PIR: S 26019 description: including ID, accession

Gene Sequence | SRS would display the PIR: S 26019 description: including ID, accession number, description, keywords, etc H K U Computer Centre

Gene Sequence | Scroll down to see the reference related to this sequence, there

Gene Sequence | Scroll down to see the reference related to this sequence, there is also a Medline reference hyperlink available H K U Computer Centre

Gene Sequence down to see the gene and the gene sequence | Scroll H

Gene Sequence down to see the gene and the gene sequence | Scroll H K U Computer Centre function

Gene Sequence | | H K U Computer Centre Save the gene sequence information

Gene Sequence | | H K U Computer Centre Save the gene sequence information to your local machine Click the “Save” button at the leftmost panel

Gene Sequence | H K U Computer Centre Click the “Output text/html format to”

Gene Sequence | H K U Computer Centre Click the “Output text/html format to” button to choose the

Gene Sequence | H K U Computer Centre Click the “Use View” button to

Gene Sequence | H K U Computer Centre Click the “Use View” button to choose the “Complete entries” format

Gene Sequence | H K U Computer Centre Then click “save” to save again

Gene Sequence | H K U Computer Centre Then click “save” to save again the PIR: S 26019 to your local machine

Simple query: Exercise 15 Minutes Break H K U Computer Centre Please try the

Simple query: Exercise 15 Minutes Break H K U Computer Centre Please try the following exercises by yourself!

Simple query: Exercise Question 1. H K U Computer Centre | Search all the

Simple query: Exercise Question 1. H K U Computer Centre | Search all the “SARS virus” in EMBL databases

Simple query: Exercise | 1. Search all the “SARS virus” in EMBL databases H

Simple query: Exercise | 1. Search all the “SARS virus” in EMBL databases H K U Computer Centre

Simple query: Exercise | 1. Search all the “SARS virus” in EMBL databases H

Simple query: Exercise | 1. Search all the “SARS virus” in EMBL databases H K U Computer Centre

Simple query: Exercise | 1. Search all the “SARS virus” in EMBL databases: H

Simple query: Exercise | 1. Search all the “SARS virus” in EMBL databases: H K U Computer Centre

Simple query: Exercise Question 2. H K U Computer Centre | How many CDS

Simple query: Exercise Question 2. H K U Computer Centre | How many CDS regions for the “EMBL: AY 278488” (SARS coronavirus BJ 01) ?

Simple query: Exercise | 2. H K U Computer Centre Click to see the

Simple query: Exercise | 2. H K U Computer Centre Click to see the detail AY 278488

Simple query: Exercise | 2. H K U Computer Centre Click to see the

Simple query: Exercise | 2. H K U Computer Centre Click to see the detail AY 278488

Simple query: Exercise | 2. H K U Computer Centre Count the number of

Simple query: Exercise | 2. H K U Computer Centre Count the number of CDS entries

Simple query: Exercise | 2. H K U Computer Centre CDS entries of EMBL:

Simple query: Exercise | 2. H K U Computer Centre CDS entries of EMBL: AY 278488 | orf 1 ab | orf 1 a polyprotein | spike glycoprotein S | putative uncharacterized | envelope protein E | membrane protein M | putative uncharacterized | nucleocapsid protein N | putative uncharacterized protein 1 protein 2 protein 3 protein 4 protein 5

Simple query: Exercise Question 3. H K U Computer Centre | What is the

Simple query: Exercise Question 3. H K U Computer Centre | What is the protein ID for EMBL: AY 278741 (SARS coronavirus Urbani) spike glycoprotein?

Simple query: Exercise | 3. H K U Computer Centre Click to see the

Simple query: Exercise | 3. H K U Computer Centre Click to see the detail AY 278741

Simple query: Exercise | 3. H K U Computer Centre EMBL: AY 278741

Simple query: Exercise | 3. H K U Computer Centre EMBL: AY 278741

Simple query: Exercise | 3. H K U Computer Centre EMBL: AY 278741

Simple query: Exercise | 3. H K U Computer Centre EMBL: AY 278741

Simple query: Exercise Question 4. H K U Computer Centre | Following the link

Simple query: Exercise Question 4. H K U Computer Centre | Following the link of the spike glycoprotein of EMBL: AY 278741, what is the biological function of this spike-protein?

Simple query: Exercise | 4. H K U Computer Centre EMBL: AY 278741

Simple query: Exercise | 4. H K U Computer Centre EMBL: AY 278741

Simple query: Exercise | 4. H K U Computer Centre Find biological function of

Simple query: Exercise | 4. H K U Computer Centre Find biological function of VGL 2_CVHSA

Simple query: Exercise | 4. H K U Computer Centre Find biological function of

Simple query: Exercise | 4. H K U Computer Centre Find biological function of VGL 2_CVHSA

Introduction to SRS H K U Computer Centre Part 2. Extended Search

Introduction to SRS H K U Computer Centre Part 2. Extended Search

Extended Search | H K U Computer Centre Click the “Select Databanks” button at

Extended Search | H K U Computer Centre Click the “Select Databanks” button at the top to select PIR as query targe

Extended Search | H K U Computer Centre Click the “Query” button at the

Extended Search | H K U Computer Centre Click the “Query” button at the top to back to query form

Extended Search | H K U Computer Centre Click the “Extended Query” button at

Extended Search | H K U Computer Centre Click the “Extended Query” button at the left panel to display the extended search form

Extended Search | | H K U Computer Centre In the “Extended” search form,

Extended Search | | H K U Computer Centre In the “Extended” search form, find the “Super Family” field and then enter “cytochrome-c ” Click the “Search” to start the query

Extended Search | H K U Computer Centre After searching for awhile, there would

Extended Search | H K U Computer Centre After searching for awhile, there would be extended search result list appear

Using Search Results | H K U Computer Centre Click the “Result” button at

Using Search Results | H K U Computer Centre Click the “Result” button at the top to reuse your query result

Using Search Results | H K U Computer Centre In the “Result” pages, enter

Using Search Results | H K U Computer Centre In the “Result” pages, enter “Q 1 !Q 3” at the top blank field and click “Expression” to combine 2 queries results(Q 1 but not Q 3), click “Search”

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

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” | H K U Computer Centre

Extended Search: Exercise 15 Minutes Break H K U Computer Centre Please try the

Extended Search: Exercise 15 Minutes Break H K U Computer Centre Please try the following exercises by yourself!

Extended Search : Exercise Question 1. H K U Computer Centre | Search all

Extended Search : Exercise Question 1. H K U Computer Centre | Search all the human DNA sequence entries created after 01 -Jan-2003 with sequence length greater than 100000 in EMBL.

Extended Search : Exercise Question 1. H K U Computer Centre

Extended Search : Exercise Question 1. H K U Computer Centre

Extended Search : Exercise Question 1. H K U Computer Centre

Extended Search : Exercise Question 1. H K U Computer Centre

Extended Search : Exercise Question 1. H K U Computer Centre

Extended Search : Exercise Question 1. H K U Computer Centre

Extended Search : Exercise Question 1. H K U Computer Centre

Extended Search : Exercise Question 1. H K U Computer Centre

Extended Search : Exercise Question 1. H K U Computer Centre

Extended Search : Exercise Question 1. H K U Computer Centre

Extended Search : Exercise Question 2. H K U Computer Centre | Search all

Extended Search : Exercise Question 2. H K U Computer Centre | Search all the mouse protein sequence entries created before 01 -Jul-2002 with NCBI TAX_ID less than 4000 in SWISSPROT.

Extended Search : Exercise Question 2. H K U Computer Centre

Extended Search : Exercise Question 2. H K U Computer Centre

Extended Search : Exercise Question 2. H K U Computer Centre

Extended Search : Exercise Question 2. H K U Computer Centre

Extended Search : Exercise Question 2. H K U Computer Centre

Extended Search : Exercise Question 2. H K U Computer Centre

Extended Search : Exercise Question 2. H K U Computer Centre

Extended Search : Exercise Question 2. H K U Computer Centre

Extended Search : Exercise Question 3. H K U Computer Centre | Using the

Extended Search : Exercise Question 3. H K U Computer Centre | Using the previous result, search the entries that have links to “PROSITE” database.

Extended Search : Exercise Question 3. Identify the Query ID (Q 6 in this

Extended Search : Exercise Question 3. Identify the Query ID (Q 6 in this case, you may not have same query ID) H K U Computer Centre

Extended Search : Exercise Question 3. Enter the expression to find the entries in

Extended Search : Exercise Question 3. Enter the expression to find the entries in previous that have link to “PROSITE” database (“Q 6<PROSITE” in this case, you may not have same query ID) H K U Computer Centre

Extended Search : Exercise Question 3. Result similar to this one H K U

Extended Search : Exercise Question 3. Result similar to this one H K U Computer Centre

Introduction to SRS H K U Computer Centre Part 3. Linking related sequence /

Introduction to SRS H K U Computer Centre Part 3. Linking related sequence / database

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

Linking Related Sequence | Go back to result #3, Click to select the first two sequence | Click “Link” button to search for the related sequence H K U Computer Centre

Linking Related Sequence H K U Computer Centre | Ensure the choice “Find related

Linking Related Sequence H K U Computer Centre | Ensure the choice “Find related entries” | Click “EMBL” as to search related sequence in this databank | Click “Search” button

Linking Related Sequence | H K U Computer Centre Result: 5 entries found in

Linking Related Sequence | H K U Computer Centre Result: 5 entries found in “EMBL” are the related sequence with your selected sequence

Linking Related Sequence | H K U Computer Centre Refine the result list to

Linking Related Sequence | H K U Computer Centre Refine the result list to “Seq. Simple. View” in the left panel

Linking Related Sequence | H K U Computer Centre Result List

Linking Related Sequence | H K U Computer Centre Result List

Linking database: Exercise 15 Minutes Break H K U Computer Centre Please try the

Linking database: Exercise 15 Minutes Break H K U Computer Centre Please try the following exercises by yourself!

Linking database: Exercise H K U Computer Centre Question 1. Find in the EMBL

Linking database: Exercise H K U Computer Centre Question 1. Find in the EMBL database the corresponding sequences that link to the longest sequence of the previous result (question #2 in extended search)

Linking database : Exercise Question 1. Go back to the previous result Question #2

Linking database : Exercise Question 1. Go back to the previous result Question #2 in extended search(Query #6 in this case) H K U Computer Centre

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

Linking database : Exercise Question 1. Sort to find the longest sequence from the result list H K U Computer Centre

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

Linking database : Exercise Question 1. Sort to find the longest sequence from the result list H K U Computer Centre

Linking database : Exercise Question 1. Click the “Link” button after selecting the longest

Linking database : Exercise Question 1. Click the “Link” button after selecting the longest sequence H K U Computer Centre

Linking database : Exercise Question 1. Search the “EMBL” database which have related entries

Linking database : Exercise Question 1. Search the “EMBL” database which have related entries links to selected sequence H K U Computer Centre

Linking database : Exercise Question 1. EMBL: AP 000423 is matched H K U

Linking database : Exercise Question 1. EMBL: AP 000423 is matched H K U Computer Centre

Linking database: Exercise H K U Computer Centre Question 2. Using the previous result

Linking database: Exercise H K U Computer Centre Question 2. Using the previous result (question #1 in simple query), make a query to find the entries which have links to SWISSPROT database

Linking database : Exercise Question 2. Go back to the previous result Question #1

Linking database : Exercise Question 2. Go back to the previous result Question #1 in simple query (Query #2 in this case) H K U Computer Centre

Linking database : Exercise Question 2. Click the “Link” button with “Unselected only” H

Linking database : Exercise Question 2. Click the “Link” button with “Unselected only” H K U Computer Centre

Linking database : Exercise Question 2. Select “Swissprot”, show only results with related entries

Linking database : Exercise Question 2. Select “Swissprot”, show only results with related entries link to “Swissprot” H K U Computer Centre

Linking database : Exercise Question 2. Around 11 EMBL entries are matched Return list

Linking database : Exercise Question 2. Around 11 EMBL entries are matched Return list should be EMBL entries but not SWISSPROT entries H K U Computer Centre

Linking database: Exercise H K U Computer Centre Question 3. Using the previous result

Linking database: Exercise H K U Computer Centre Question 3. Using the previous result (question #1 in simple query), make a query to find the entries which have no links to SWISSPROT database

Linking database : Exercise Question 3. Select “Swissprot”, show only results without related entries

Linking database : Exercise Question 3. Select “Swissprot”, show only results without related entries H K U Computer Centre

Linking database : Exercise Question 3. Around 32 EMBL entries are matched H K

Linking database : Exercise Question 3. Around 32 EMBL entries are matched H K U Computer Centre

Introduction to SRS H K U Computer Centre Part 4. Application

Introduction to SRS H K U Computer Centre Part 4. Application

Application: BLAST Go back to the query result page -> Q 9 "(([PIR-ID: ODHU

Application: BLAST Go back to the query result page -> Q 9 "(([PIR-ID: ODHU 1] | [PIR-ID: ODBO 1]) > EMBL )" | Click the checkbox of EMBL: MIHSM 1 and then click “Launch” with application “BLASTN” | H K U Computer Centre

Application: BLAST | BLAST window appear and change the “Complete Database to search” to

Application: BLAST | BLAST window appear and change the “Complete Database to search” to Genome | H K U Computer Centre Yeast Complete Change other parameters as you like and then click “Launch” to execute

Application: BLAST H K U Computer Centre | BLAST job was submitted to the

Application: BLAST H K U Computer Centre | BLAST job was submitted to the batch queue | Click the hourglass icon (left top corner) to check whether the job is

Application: BLAST | After H K U Computer Centre the job result is ready,

Application: BLAST | After H K U Computer Centre the job result is ready, click to see the BLA

Application: BLAST | H K U Computer Centre After waiting for awhile, the BLAST

Application: BLAST | H K U Computer Centre After waiting for awhile, the BLAST result list appear, click any one of them to view the detail

Application: BLAST | H K U Computer Centre BLAST alignment result with the databanks

Application: BLAST | H K U Computer Centre BLAST alignment result with the databanks

Application: Clustalw | Go back to blast result list. Then click the checkbox to

Application: Clustalw | Go back to blast result list. Then click the checkbox to select first 5 sequence | Click the Application pull down menu to “ and then click “ H K U Computer Centre Launch” NClustal. W”

Application: Clustalw | H K U Computer Centre Then “Clustal. W” window appear and

Application: Clustalw | H K U Computer Centre Then “Clustal. W” window appear and change the parameters as you like

Application: Clustalw | H K U Computer Centre Launch After click “ ”, SRS

Application: Clustalw | H K U Computer Centre Launch After click “ ”, SRS would launch clustalw with you selected sequence and give the result

Application: EMBOSS(eg: PRETTYPLOT) | H K U Computer Centre Using the Clustal. W result,

Application: EMBOSS(eg: PRETTYPLOT) | H K U Computer Centre Using the Clustal. W result, and then click “Tools”

Application: EMBOSS(eg: PRETTYPLOT) | H K U Computer Centre Choose “prettyplot. N” , and

Application: EMBOSS(eg: PRETTYPLOT) | H K U Computer Centre Choose “prettyplot. N” , and then click “Launch”

Application: EMBOSS(eg: PRETTYPLOT) | H K U Computer Centre It jump to “prettyplot. N”

Application: EMBOSS(eg: PRETTYPLOT) | H K U Computer Centre It jump to “prettyplot. N” interface, scroll down …. .

Application: EMBOSS(eg: PRETTYPLOT) | H K U Computer Centre Click to select “Display the

Application: EMBOSS(eg: PRETTYPLOT) | H K U Computer Centre Click to select “Display the consensus”, and then click “Launch”

Application: EMBOSS(eg: PRETTYPLOT) | H K U Computer Centre Click the first graphic file

Application: EMBOSS(eg: PRETTYPLOT) | H K U Computer Centre Click the first graphic file to view the result, while the second file would be empty

Application: EMBOSS(eg: PRETTYPLOT) | | H K U Computer Centre You will see the

Application: EMBOSS(eg: PRETTYPLOT) | | H K U Computer Centre You will see the identical residue shown in RED color The last line show the consensus of the alignment

Application: EMBOSS(eg: SIXPACK) Go back to the query result page -> Q 9 "(([PIR-ID:

Application: EMBOSS(eg: SIXPACK) Go back to the query result page -> Q 9 "(([PIR-ID: ODHU 1] | [PIR-ID: ODBO 1]) > EMBL )" | Click the checkbox of EMBL: MIHSM 1 and then click “Tools” | H K U Computer Centre

Application: EMBOSS(eg: SIXPACK) | H K U Computer Centre Choose “SIXPACK” and then click

Application: EMBOSS(eg: SIXPACK) | H K U Computer Centre Choose “SIXPACK” and then click “Launch”

Application: EMBOSS(eg: SIXPACK) | H K U Computer Centre click “Launch” to run SIXPACK

Application: EMBOSS(eg: SIXPACK) | H K U Computer Centre click “Launch” to run SIXPACK program

Application: EMBOSS(eg: SIXPACK) | H K U Computer Centre At the result page, see

Application: EMBOSS(eg: SIXPACK) | H K U Computer Centre At the result page, see the number of possible ORF in 6 -frame

Application: EMBOSS(eg: SIXPACK) | H K U Computer Centre See the translation in all

Application: EMBOSS(eg: SIXPACK) | H K U Computer Centre See the translation in all 6 -frames

Application: EMBOSS(eg: TMAP) Several EMBOSS can be directly launched by SRS: for example, TMAP

Application: EMBOSS(eg: TMAP) Several EMBOSS can be directly launched by SRS: for example, TMAP | Go back to Q 4 result and click the checkbox of PIR: S 26019 and then click “Tools” | H K U Computer Centre

| H K U Computer Centre Application: EMBOSS(eg: TMAP) It will jump to show

| H K U Computer Centre Application: EMBOSS(eg: TMAP) It will jump to show a list of application, change the pull-down menu to “TMAP” TMAP and click launch

| H K U Computer Centre Application: EMBOSS(eg: TMAP) “TMAP” window appear and click

| H K U Computer Centre Application: EMBOSS(eg: TMAP) “TMAP” window appear and click “Launch” to execute TMAP with your selected sequence

| H K U Computer Centre Application: EMBOSS(eg: TMAP) After waiting for awhile, “TMAP”give

| H K U Computer Centre Application: EMBOSS(eg: TMAP) After waiting for awhile, “TMAP”give out the predicts transmembrane segments result

| H K U Computer Centre Application: EMBOSS(eg: TMAP) Scroll at the bottom to

| H K U Computer Centre Application: EMBOSS(eg: TMAP) Scroll at the bottom to click to see the membrane spanning regions diagram

Application : Exercise 15 Minutes Break H K U Computer Centre Please try the

Application : Exercise 15 Minutes Break H K U Computer Centre Please try the following exercises by yourself!

Application: Exercise H K U Computer Centre Question 1. Do the sequence alignment of

Application: Exercise H K U Computer Centre Question 1. Do the sequence alignment of the 5 shortest sequence from the previous result (question #2 in extended search) using clustalw

Application: Exercise Question 1. Go back to the previous result Question #2 in extended

Application: Exercise Question 1. Go back to the previous result Question #2 in extended search, Q 6 in this case H K U Computer Centre

Application: Exercise Question 1. Sort to find the 5 shortest sequences from the result

Application: Exercise Question 1. Sort to find the 5 shortest sequences from the result list H K U Computer Centre

Application: Exercise Question 1. Launch “Clustalw” after selecting 5 shortest sequences H K U

Application: Exercise Question 1. Launch “Clustalw” after selecting 5 shortest sequences H K U Computer Centre

Application: Exercise Question 1. No need to modify any parameters, click “launch” to start

Application: Exercise Question 1. No need to modify any parameters, click “launch” to start sequence alignment H K U Computer Centre

Application: Exercise Question 1. H K U Computer Centre

Application: Exercise Question 1. H K U Computer Centre

Application: Exercise H K U Computer Centre Question 2. Do the BLAST search using

Application: Exercise H K U Computer Centre Question 2. Do the BLAST search using the EMBL: AY 278491 (HKU-SARS virus) sequence against EMBL (Release): VRL(virus) database

Application: Exercise Question 2. Go back to previous result list(Q 2 in normal case)

Application: Exercise Question 2. Go back to previous result list(Q 2 in normal case) to find the HKU-SARS virus H K U Computer Centre

Application: Exercise Question 2. Search against the Viruses database H K U Computer Centre

Application: Exercise Question 2. Search against the Viruses database H K U Computer Centre

Application: Exercise Question 2. After waiting for few minutes, BLAST result list display H

Application: Exercise Question 2. After waiting for few minutes, BLAST result list display H K U Computer Centre

Application: Exercise Question 2. See the BLAST result vs TOR 2 H K U

Application: Exercise Question 2. See the BLAST result vs TOR 2 H K U Computer Centre

Application: Exercise H K U Computer Centre Question 3. Find the transmembrance segments of

Application: Exercise H K U Computer Centre Question 3. Find the transmembrance segments of the SWISSPROT: VME 1_CVHSA (SARS virus M-protein) sequence using TMAP

Application: Exercise Question 3. After finding the sequence, launch “tmap” H K U Computer

Application: Exercise Question 3. After finding the sequence, launch “tmap” H K U Computer Centre

Application: Exercise Question 3. After finding the sequence, launch “tmap” H K U Computer

Application: Exercise Question 3. After finding the sequence, launch “tmap” H K U Computer Centre

Application: Exercise Question 3. H K U Computer Centre

Application: Exercise Question 3. H K U Computer Centre

Application: Exercise Question 3. H K U Computer Centre

Application: Exercise Question 3. H K U Computer Centre

Application: Exercise Question 3. H K U Computer Centre

Application: Exercise Question 3. H K U Computer Centre

Introduction to SRS H K U Computer Centre Part 5. Others

Introduction to SRS H K U Computer Centre Part 5. Others

User submit own sequence: User can submit their own sequence to work with SRS

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 | H K U Computer Centre

User submit own sequence: | | H K U Computer Centre Enter your own

User submit own sequence: | | H K U Computer Centre Enter your own DNA sequence in the blank field Then click “Launch” to input your own sequence to the User. DNA databank

User submit own sequence: | H K U Computer Centre Wait for SRS to

User submit own sequence: | H K U Computer Centre Wait for SRS to store your input DNA sequence

User submit own sequence: | H K U Computer Centre Your sequence has been

User submit own sequence: | H K U Computer Centre Your sequence has been successfully input to the USERDNA databank

User submit own sequence: Then you can search related link sequence or launch application

User submit own sequence: Then you can search related link sequence or launch application with your sequence | For example, you can launch BLAST with your input sequence | H K U Computer Centre

SRS On-Line Help H K U Computer Centre

SRS On-Line Help H K U Computer Centre

SRS On-Line Help H K U Computer Centre

SRS On-Line Help H K U Computer Centre

H K U Computer Centre -END-

H K U Computer Centre -END-