http://www.fludb.org/

Freely available Integrated datasets Bioinformatics tool suite Platform for influenza data submission

IRD is funded by the National Institute of Allergy and Infectious Diseases (NIH/DHHS) under Contract No. HHSN266200400041C and is a collaboration between Northrop Grumman Health IT, University of Texas Southwestern Medical Center , Vecna Technologies, SAGE Analytica and Los Alamos National Laboratory. Comments, questions, suggestions? Contact us at feedback@virusbrc.org

Multiple Sequence Alignment (MSA)

Option 1: Search for sequences and then align sequences

Choose sequences for alignment Run the alignment

Customize the alignment based on

your need

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2

1. Identify sequences to align: mouse-over the “Search Data” tab and click “Nucleotide Sequences” or “Protein Sequences”. For this example, we will use nucleotide sequences.

2. Select search criteria on the Nucleotide Sequence Search page and click the “Search” button to run your query.

3. Select sequences from the search result page by clicking the checkboxes. Mouse-over the yellow “Run Analysis” button and click “Align Sequences (MSA)”. If you want to include sequences that are not in this search result or to use the sequences to do further analysis, select the desired sequences and click “Add to Working Set”. Then add other sequences to the same working set later by repeating the process. Click the “Workbench” tab and find the working set you saved. Click

next to it to view the details of the working set. Then mouse-over the yellow “Run Analysis” button and click “Align Sequences (MSA).

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3

Click to view details of

the record

• Select display fields • Custom-sort records

Select sequences and add them to a working set for future analysis. You’ll need to register a Workbench account

to use this feature.

Cite IRD Tutorials Glossary of Terms Report a Bug Request Web Training Contact Us Release Date: Jul 18, 2011

This project is funded by the National Institute of Allergy and Infectious Diseases (NIH / DHHS) under Contract No. HHSN266200400041C and is a collaboration between NorthropGrumman Health IT, University of Texas Southwestern Medical Center , Vecna Technologies, SAGE Analytica and Los Alamos National Laboratory.

2 records were previously selected from search results

INPUT SEQUENCESHTML

SELECT OUTPUT FORMATAligned

SELECT OUTPUT ORDER

RunClear

Align Sequences (MSA) IRD uses the MUSCLE (Multiple Sequence Comparison by Log-Expectation) algorithm to align the sequences you select from a search result or a working set on yourworkbench or that you provide in an uploaded file.

Home Nucleotide Sequence Search Results Align Sequences (MSA)

SEARCH DATA ANALYZE & VISUALIZE WORKBENCH SUBMIT DATA HOME

About Us Community Announcements Links Resources Support Sign Out

You are logged in as yun.zhang@utsouthwestern.edu

Inuenza Research Database - MUSCLE Multiple Sequence Alig... http://www.udb.org/brc/msa.do

1 of 1 8/1/11 4:27 PM

5

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6

4

4. A “Select Sequence Type” lightbox will pop-up. Select the appropriate sequence type and click “Continue”.

5. On the next page, select output format and output order. Then click “Run”.

6. If you have a large amount of input to align, the analysis may take a few minutes to run. While the analysis is running, you can choose to save it (upon completion) to your Workbench by entering a name for the analysis and then clicking the “Save to Workbench” button. Then you can move to other parts of the IRD site, and retrieve the alignment later from your Workbench.

2

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http://www.fludb.org/

Freely available Integrated datasets Bioinformatics tool suite Platform for influenza data submission

IRD is funded by the National Institute of Allergy and Infectious Diseases (NIH/DHHS) under Contract No. HHSN266200400041C and is a collaboration between Northrop Grumman Health IT, University of Texas Southwestern Medical Center , Vecna Technologies, SAGE Analytica and Los Alamos National Laboratory. Comments, questions, suggestions? Contact us at feedback@virusbrc.org

Option 2: Align sequences from a working set or your own sequences

!"#$%&'( )*#+,"-./ 0.+//-,1%+2%)$,3/ '$4+,#%-%5*6 '$7*$/#%8$9%),-":":6 !+:#-;#%</ '$.$-/$%(-#$=%>*.%?@A%BC??

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1

Loading Influenza Research Database...

Cite IRD Tutorials Glossary of Terms Report a Bug Request Web Training Contact Us Release Date: Jul 18, 2011

This project is funded by the National Institute of Allergy and Infectious Diseases (NIH / DHHS) under Contract No. HHSN266200400041C and is a collaboration between NorthropGrumman Health IT, University of Texas Southwestern Medical Center , Vecna Technologies, SAGE Analytica and Los Alamos National Laboratory.

Upload a file containing my sequences in FASTA format.

Paste sequence in FASTA format.

Use working set.

INPUT SEQUENCESSequences can also be selected from search results or a working set in yourworkbench.

File Path:Browse�…

The minimum number of sequences is 2.

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SELECT OUTPUT FORMATAligned

SELECT OUTPUT ORDER

RunClear

Align Sequences (MSA) IRD uses the MUSCLE (Multiple Sequence Comparison by Log-Expectation) algorithm to align the sequences you select from a search result or a working set on yourworkbench or that you provide in an uploaded file.

Home Align Sequences (MSA)

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Inuenza Research Database - MUSCLE Multiple Sequence Alig... http://www.udb.org/brc/msa.do?method=ShowCleanInputPage&...

1 of 1 8/1/11 3:10 PM

2

2.1

Three options to input sequences

Visualize and Customize the Alignment

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2.3

Loading Influenza Research Database...

Cite IRD Tutorials Glossary of Terms Report a Bug Request Web Training Contact Us Release Date: Jul 18, 2011

This project is funded by the National Institute of Allergy and Infectious Diseases (NIH / DHHS) under Contract No. HHSN266200400041C and is a collaboration between NorthropGrumman Health IT, University of Texas Southwestern Medical Center , Vecna Technologies, SAGE Analytica and Los Alamos National Laboratory.

Upload a file containing my sequences in FASTA format.

Paste sequence in FASTA format.

Use working set.

INPUT SEQUENCESSequences can also be selected from search results or a working set in your workbench.

>gb:HM628693|Organism:Influenza A virus A/Acre/15093/2010|Segment:4|Subtype:H3N2|Host:HumanATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCTCAAAAACTTCCTGGAAATGACAACAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGGACGATAGTGAAAACAATCACGAATGACCAAATTGAAGTTACTTATGCTACTGAGCTGGTTCAGAGTTCCTCAACAGGTGAAATATGCGACAGTCCCCATCAGATCCTTGATGGAAAAAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTCCAAAATAAGAAATGGGACCTTTTTGTTGAACGCAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACACTTGAGTTTAACAATGAAAGC

The minimum number of sequences is 2.Defline in your FASTA file will be used to label the display

HTML

SELECT OUTPUT FORMATAligned

SELECT OUTPUT ORDER

RunClear

Align Sequences (MSA) IRD uses the MUSCLE (Multiple Sequence Comparison by Log-Expectation) algorithm to align the sequences you select from a search result or a working set on yourworkbench or that you provide in an uploaded file.

Home Align Sequences (MSA)

SEARCH DATA ANALYZE & VISUALIZE WORKBENCH SUBMIT DATA HOME

About Us Community Announcements Links Resources Support Sign Out

You are logged in as yun.zhang@utsouthwestern.edu

Inuenza Research Database - MUSCLE Multiple Sequence Alig... http://www.udb.org/brc/msa.do?method=ShowCleanInputPage&...

1 of 1 8/1/11 4:10 PM

2.2

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3

1. Mouse-over the “Analyze & Visualize” tab and click “Align Sequences (MSA)”.

2. On the MSA landing page, use one of the three options to input sequences:

2.1 Upload a file containing sequences in FASTA format. 2.2 Paste sequences in FASTA format. 2.3 Use a working set from your Workbench.

Select output format and order. Then click “Run”. 3. If you have a large amount of input, the analysis may

take a few minutes to run. While the analysis is running, you can choose to save it (upon completion) to your Workbench by entering a name for the analysis and then clicking the “Save to Workbench” button. Then you can move to other parts of the IRD site, and retrieve the alignment later from your Workbench.

1. After the alignment analysis is finished, mouse-over “Run Analysis” and click “Visualize Aligned Sequences”.

2. On the next page, you will have the option to customize the sequence labels by selecting the “Custom” radio button in the “Label sequence by” section. Click “Run” to load the alignment visualization window.

3. In the alignment visualization window, many customization options exist: • Rename a sequence label: Right-click a strain name in the alignment,

mouse-over the sequence name in pop-up menu, click “Edit Name/Description”, modify the name and click “Accept”.

• Highlight IRD-defined Sequence Features on the alignment: • Add your own sequence feature to the alignment: Click and drag a desired

region of sequence alignment, right-click the selected region, mouse-over “Selection” and click “Create Sequence Feature”.

• Color alignment based on sequence identity cutoff: Click the “Colour” pulldown menu and then the “Above Identity Threshold” option. Using sliding bar to adjust color display.

• Manually adjust the alignment: Click a sequence and then use ç èon the keyboard to adjust the alignment.

4. Export the alignment from the “File” menu.

1

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2

Select and highlight IRD-defined Sequence

Features on the alignment

Export the alignment

Add your own sequence feature on

the alignment

Rename a sequence label

3