sequence conservation/variation analysis
TRANSCRIPT
Cite IRD Tutorials Glossary of Terms Report a Bug Request Web Training Contact Us Release Date: Sep 7, 2012
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, J. Craig Venter Institute , Vecna Technologies, SAGE Analytica and Los Alamos National Laboratory.
Human
HOSTH1N1
SUB TYPEGenomic Sequence Analysis
ANALYSIS1
SEGMENT/PROTEIN
RunClear
SEARCH TYPE Precomputed analysis using sequences in the IRD database for a specified host, segment, and subtype New analysis of sequences you select from the IRD database or upload
To study sequence polymorphism across different influenza A strains, all influenza type A sequences were downloaded from GenBank. These sequences were processedthrough the IRD curation pipeline. During this processing, pre-aligned sequences were generated with the ClustalW multiple alignment tool. Aligned sequences from thesame host and segment (and subtype) were used to determine sequence polymorphism.
A consensus sequence for each subtype was created by following the majority rule. For each position in the nucleotide multiple alignment, a score was generated by using aformula modified from the one as described in Crooks et al.. The score ranges from 0 (no polymorphism) to 200 (highest polymorphism). For more details on the scoreand general polymorphism approach, reference our Help document.
SEARCH CRITERIA
Analyze Sequence Variation (SNP) The IRD team has grouped sequences by segment number, flu type, subtype, and host and aligned the sequences. A consensus sequence has been determined for each groupand the variation from that value has been determined for each position in the sequence. This has been done for both nucleotide and amino acid sequences. The IRD tool canperform the same analysis using nucleotide or amino acid sequences that you either select from the IRD database or upload on this page.
Home Analyze Sequence Variation
SEARCH DATA ANALYZE & VISUALIZE WORKBENCH SUBMIT DATA
About Us Community Announcements Links Resources Support Sign Out
You are logged in as [email protected]
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 under Contract No. HHSN266200400041C and is a collaboration between Northrop Grumman Health IT, J. Craig Venter Institute, Vecna Technologies, SAGE Analytica and Los Alamos National Laboratory. University of Texas Southwestern Medical Center was a past subcontractor. Questions, suggestions? Contact us at [email protected]
Sequence Conservation/Variation Analysis
I. Examine consensus sequence/sequence polymorphism across all influenza A strains
1 2
You can view the consensus and all sequence variations existing in all GenBank influenza type A sequences based on host of isolation, flu subtype and segment.
• Lets you analyze sequence polymorphism at the nucleotide or amino acid level. • Provides pre-computed consensus sequence and polymorphism score at each
position for all influenza A strains. • Allows you to calculate polymorphism of IRD sequences or your own sequences.
Select host, influenza subtype, type of sequence
to analyze, segment number or protein name.
Figure View Protein Sequence Analysis (4 HA) FASTA Format Raw Alignment
Sequence Variance Analysis for Human H1N1, Segment 4
Position Coding Score Consensus A T G C Deletion # Sequences
1 no 72 A 683 6 129 3 0 821
2 no 70 G 5 2 720 136 0 863
3 no 73 C 132 0 15 730 0 877
4 no 12 A 882 2 10 1 0 895
5 no 5 A 927 0 3 2 0 932
6 no 6 A 939 1 2 2 0 944
7 no 66 A 801 1 145 3 0 950
8 no 69 G 6 1 803 147 1 958
9 no 66 C 149 0 6 844 0 999
10 no 67 A 853 1 150 2 3 1009
11 no 7 G 3 1 1043 3 0 1050
12 no 5 G 2 2 1197 2 0 1203
13 no 6 G 7 0 1502 2 0 1511
14 no 69 G 313 0 1412 1 0 1726
15 no 6 A 1839 2 8 1 0 1850
16 no 27 A 2027 88 3 1 0 2119
17 no 3 A 2250 1 3 3 0 2257
18 no 66 A 1995 32 6 275 0 2309
19 no 158 N 751 1037 2 1028 0 2818
20 no 8 A 4054 13 5 3 9 4084
21 no 2 A 4150 0 4 4 0 4158
22 no 2 A 4200 2 0 3 1 4206
23 no 69 A 3543 4 778 1 0 4326
24 no 138 G 904 3 2604 831 0 4342
25 no 69 C 787 1 2 3565 0 4355
26 no 3 A 4354 2 5 4 1 4366
27 no 69 A 3611 2 1 792 0 4406
28 no 69 C 779 6 0 3660 2 4447
29 no 123 A 2872 6 1 1224 368 4471
30 no 7 A 4499 4 28 2 0 4533
31 no 38 A 4228 3 325 1 1 4558
32 no 45 A 4169 1 9 1 400 4580
33 no 0 A 11497 0 2 0 0 11499
34 no 0 T 2 11498 1 0 0 11501
35 no 0 G 1 0 11503 0 0 11504
36 no 19 A 11190 0 331 0 0 11522
37 no 1 A 11519 2 4 1 0 11526
38 no 84 G 3006 4 8518 2 0 11531
39 no 2 G 24 1 11509 0 1 11535
40 no 73 C 2 2319 1 9213 1 11539
41 no 7 A 11458 4 77 2 1 11542
42 no 1 A 11579 0 4 0 1 11584
43 no 87 T 3057 8489 30 16 1 11594
44 no 5 A 11535 2 4 57 1 11599
45 no 2 C 12 9 0 11583 1 11606
Home Analyze Sequence Variation Results
SEARCH DATA ANALYZE & VISUALIZE WORKBENCH SUBMIT DATA
About Us Community Announcements Links Resources Support Sign Out
You are logged in as [email protected]
3
At each position, the consensus is the allele with
frequency greater than 50%. If no allele exceeds 50%, N (for nucleotide) or Xaa (for
amino acid) is used to indicate ambiguity.
Switch to protein sequence
variation result analysis result
Download consensus sequence
in FASTA format
Download raw alignment of all
sequences
Score ranges from 0 (no
polymorphism) to 200 (highest
polymorphism).
Count for different
nucleotides at each position
View sequence polymorphism
plot
1. Mouse-over the “Analyze & Visualize” tab and click “Analyze Sequence Variation (SNP)”.
2. On the tool landing page, select “Pre-computed analysis using sequences in the IRD database for a specified host, segment, and subtype” in search type. Next, select desired host, subtype, analysis type (genomic or protein sequence), and segment/protein to analyze. Click “Run”.
3. The analysis result page will be loaded, which shows the polymorphism score, consensus, and counts for each different base/amino acid at each position. Sequence polymorphism plot, consensus sequence, and raw alignment are available for download.
2
Cite IRD Tutorials Glossary of Terms Report a Bug Request Web Training Contact Us Release Date: Sep 7, 2012
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, J. Craig Venter Institute , Vecna Technologies, SAGE Analytica and Los Alamos National Laboratory.
Upload a file containing my sequences in FASTA format.
Paste sequences in FASTA format.
Use working sets
INPUT SEQUENCES
Sequences can also be selected from search results or a working set in your workbench.
File Path:Browse…
The minimum number of sequences is 2.
RunClear
SEARCH TYPE Precomputed analysis using sequences in the IRD database for a specified host, segment, and subtype New analysis of sequences you select from the IRD database or upload
To study sequence polymorphism across different influenza A strains, all influenza type A sequences were downloaded from GenBank. These sequences were processedthrough the IRD curation pipeline. During this processing, pre-aligned sequences were generated with the ClustalW multiple alignment tool. Aligned sequences from thesame host and segment (and subtype) were used to determine sequence polymorphism.
A consensus sequence for each subtype was created by following the majority rule. For each position in the nucleotide multiple alignment, a score was generated by using aformula modified from the one as described in Crooks et al.. The score ranges from 0 (no polymorphism) to 200 (highest polymorphism). For more details on the scoreand general polymorphism approach, reference our Help document.
Analyze Sequence Variation (SNP) The IRD team has grouped sequences by segment number, flu type, subtype, and host and aligned the sequences. A consensus sequence has been determined for each groupand the variation from that value has been determined for each position in the sequence. This has been done for both nucleotide and amino acid sequences. The IRD tool canperform the same analysis using nucleotide or amino acid sequences that you either select from the IRD database or upload on this page.
Home Analyze Sequence Variation
SEARCH DATA ANALYZE & VISUALIZE WORKBENCH SUBMIT DATA
About Us Community Announcements Links Resources Support Sign Out
You are logged in as [email protected]
Cite IRD Tutorials Glossary of Terms Report a Bug Request Web Training Contact Us Release Date: Sep 7, 2012
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, J. Craig Venter Institute , Vecna Technologies, SAGE Analytica and Los Alamos National Laboratory.
DATA TO RETURN Segment / Nucleotide
Protein
Strain
VIRUS TYPEA
B
C
SUB TYPE
* Use comma to separate multipleentries.Ex: H1N1, H7, H3N2.
STRAIN NAME
* Use comma to separate multipleentries.Ex: A/chicken/Israel/1055/2008,A/chicken/Laos/16/2008.
Complete Genome OnlyComplete SequencesInclude laboratory strainsInclude/exclude records with highsimilarity to 2009 pH1N1sequences (SOP)
SELECT SEGMENTSAll1 PB22 PB1/PB1-F23 PA/PA-X4 HA5 NP6 NA7 M1/M28 NS1/NS2
DATE RANGEFrom: YYYY To: YYYY
To add month to search, seeAdvance Options: Month Range
HOSTAllAvianBatBlow FlyCamelCheetahCivetDogDomestic CatDonkeyEnvironmentFerretHorseHumanLabLarge CatM l
GEOGRAPHIC GROUPINGAllAfricaAsiaEuropeNorth AmericaOceaniaS h A i
COUNTRYAfghanistanAlgeriaArgentinaAustraliaAustriaAzerbaijanB h i
ADVANCED OPTIONSSearchClear
Tip: To select multiple or deselect, Ctrl-click (Windows) or Cmd-click (MacOS) Show All
Nucleotide Sequence Search Search for influenza sequences, proteins, and strains using two types of searches. Use the advanced search to allow you to refine your search with the more fine grained search,and you can pick your viewing options.
205,653 matching results
Home Nucleotide Sequence Search
SEARCH DATA ANALYZE & VISUALIZE WORKBENCH SUBMIT DATA
QUICK SEARCH
Quick Search
SEARCH FOR OR FIND
Search Sequences
Animal Surveillance
Immune Epitopes
3D Protein Structures
Phenotype
Human Clinical Metadata
Serology Experiments (Beta)
Sequence Feature Variant Types (beta)
PCR Primer Probe Data
Host Factor Data (Beta)
Laboratory Experiments (beta)
WHO Influenza Vaccine Strains
SEARCH HISTORY
Retrieve a Download
Your Search History
Nucleotide Sequences
Protein Sequences
Strain Data
About Us Community Announcements Links Resources Support Sign Out
You are logged in as [email protected]
Your search returned 894 segments. Search Criteria Displaying 50 per pageDisplay Settings
Add to Working Set Save Search Download
1 2 3 4 5 6 7 Next > Page: 1 of 18
Nucleotide Sequence Search Results
Your Selected Items: 6 items selected | Deselect All
Select all 894 segments
SegmentProteinName
SequenceAccession
DateHost
SpeciesCountry
FluSeason
Strain Name
4 HA U04857 1937 Swine USA -N/A- *A/swine/29/1937(H1N1)
4 HA CY025002 1977 Swine USA -N/A- *A/swine/Arizona/148/1977(H1N1)
4 HA CY082070 No 900 H1N1 02/09/2006 *Swine USA 05-06 A/swine/Arkansas/00993/2006
4 HA CY082074 No 883 H1N1 02/23/2006 *Swine USA 05-06 A/swine/Arkansas/00998/2006
4 HA CY082359 * No 902 H1N1 01/31/2007 *Swine USA 06-07 A/swine/Arkansas/01460/2007
4 HA CY040460 No 901 H1N1 2008 Swine USA -N/A- *A/swine/Arkansas/63607-3/2008(H1N1)
4 HA CY028780 Yes 1732 H1N1 1991 Swine USA -N/A- *A/swine/California/T9001707/1991(H1N1)
4 HA CY082171 * No 859 H1N1 05/31/2006 *Swine USA 05-06 A/swine/Colorado/01151/2006
4 HA CY081685 No 895 H1N1 02/24/2004 *Swine USA 03-04 A/swine/Georgia/00252/2004
4 HA CY081707 * No 888 H1N1 05/04/2004 Swine USA 03-04 A/swine/Georgia/00297/2004
4 HA CY082071 No 904 H1N1 02/10/2006 Swine USA 05-06 A/swine/Georgia/00995/2006
4 HA FJ638298 No 1713 H1N1 2005 Swine USA -N/A- *A/swine/IL/00685/2005(H1N1)
4 HA GU984396 No 1701 H1N1 12/29/2009 Swine USA 09-10 *A/swine/IL/10-001550/2009(H1N1)
4 HA GU984399 No 1701 H1N1 12/20/2009 Swine USA 09-10 *A/swine/IL/10-001551-1/2009(H1N1)
4 HA GU984402 No 1701 H1N1 12/20/2009 Swine USA 09-10 *A/swine/IL/10-001551-2/2009(H1N1)
4 HA HM219618 No 1701 H1N1 02/23/2010 Swine USA 09-10 *A/swine/IL/12660/2010(H1N1)
4 HA HM219633 No 1701 H1N1 03/18/2010 Swine USA 09-10 *A/swine/IL/17315-1/2010(H1N1)
4 HA HM219636 No 1701 H1N1 03/18/2010 Swine USA 09-10 *A/swine/IL/17315-3/2010(H1N1)
4 HA HQ291537 No 1701 H1N1 05/18/2010 Swine USA 09-10 *A/swine/IL/25399-2/2010(H1N1)
4 HA HQ291540 No 1701 H1N1 05/18/2010 Swine USA 09-10 *A/swine/IL/25399-3/2010(H1N1)
4 HA HQ291543 No 1701 H1N1 05/18/2010 Swine USA 09-10 *A/swine/IL/25399-4/2010(H1N1)
4 HA HQ291546 No 1701 H1N1 06/02/2010 Swine USA -N/A- *A/swine/IL/27486-1/2010(H1N1)
4 HA HQ291549 No 1701 H1N1 06/02/2010 Swine USA -N/A- *A/swine/IL/27486-2/2010(H1N1)
4 HA GU480922 No 1701 H1N1 11/11/2009 Swine USA 09-10 *A/swine/IL/32974/2009(H1N1)
Run Analysis �
Home Nucleotide Sequence Search Results
Identify Similar Sequences (BLAST)
Align Sequences (MSA)
Visualize Aligned Sequences
Generate Phylogenetic Tree
Analyze Sequence Variation (SNP)
SEARCH DATA ANALYZE & VISUALIZE WORKBENCH SUBMIT DATA HOME
About Us Community Announcements Links Resources Support Sign Out
You are logged in as [email protected]
Inuenza Research Database - Nucleotide Sequence Search Results http://www.udb.org/brc/inuenza_sequence_search_segment_dis...
1 of 2 7/28/11 12:38 PM
Cite IRD Tutorials Glossary of Terms Report a Bug Request Web Training Contact Us Release Date: Sep 7, 2012
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, J. Craig Venter Institute , Vecna Technologies, SAGE Analytica and Los Alamos National Laboratory.
50 records were previously selected from search results
INPUT SEQUENCES
RunClear
To study sequence polymorphism across different influenza A strains, all influenza type A sequences were downloaded from GenBank. These sequences were processedthrough the IRD curation pipeline. During this processing, pre-aligned sequences were generated with the ClustalW multiple alignment tool. Aligned sequences from thesame host and segment (and subtype) were used to determine sequence polymorphism.
A consensus sequence for each subtype was created by following the majority rule. For each position in the nucleotide multiple alignment, a score was generated by using aformula modified from the one as described in Crooks et al.. The score ranges from 0 (no polymorphism) to 200 (highest polymorphism). For more details on the scoreand general polymorphism approach, reference our Help document.
Analyze Sequence Variation (SNP) The IRD team has grouped sequences by segment number, flu type, subtype, and host and aligned the sequences. A consensus sequence has been determined for each groupand the variation from that value has been determined for each position in the sequence. This has been done for both nucleotide and amino acid sequences. The IRD tool canperform the same analysis using nucleotide or amino acid sequences that you either select from the IRD database or upload on this page.
Home Nucleotide Sequence Search Results Analyze Sequence Variation
SEARCH DATA ANALYZE & VISUALIZE WORKBENCH SUBMIT DATA
About Us Community Announcements Links Resources Support Sign Out
You are logged in as [email protected]
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 [email protected]
Influenza Research Database - MUSCLE Multiple Sequence Alig... http://www.fludb.org/brc/msa.do?method=ShowCleanInputPage&...
1 of 1 8/1/11 4:10 PM
Cite IRD Tutorials Glossary of Terms Report a Bug Request Web Training Contact Us Release Date: Sep 7, 2012
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, J. Craig Venter Institute , Vecna Technologies, SAGE Analytica and Los Alamos National Laboratory.
Pandemic_H1N1
HOSTH1N1
SUB TYPEProtein Sequence Analysis
ANALYSIS1 PB2
SEGMENT/PROTEIN
RunClear
SEARCH TYPE Precomputed analysis using sequences in the IRD database for a specified host, segment, and subtype New analysis of sequences you select from the IRD database or upload
To study sequence polymorphism across different influenza A strains, all influenza type A sequences were downloaded from GenBank. These sequences were processedthrough the IRD curation pipeline. During this processing, pre-aligned sequences were generated with the ClustalW multiple alignment tool. Aligned sequences from thesame host and segment (and subtype) were used to determine sequence polymorphism.
A consensus sequence for each subtype was created by following the majority rule. For each position in the nucleotide multiple alignment, a score was generated by using aformula modified from the one as described in Crooks et al.. The score ranges from 0 (no polymorphism) to 200 (highest polymorphism). For more details on the scoreand general polymorphism approach, reference our Help document.
SEARCH CRITERIA
Analyze Sequence Variation (SNP) The IRD team has grouped sequences by segment number, flu type, subtype, and host and aligned the sequences. A consensus sequence has been determined for each groupand the variation from that value has been determined for each position in the sequence. This has been done for both nucleotide and amino acid sequences. The IRD tool canperform the same analysis using nucleotide or amino acid sequences that you either select from the IRD database or upload on this page.
Home Analyze Sequence Variation
SEARCH DATA ANALYZE & VISUALIZE WORKBENCH SUBMIT DATA
ANALYZE & VISUALIZE
Identify Similar Sequences (BLAST)
Align Sequences (MSA)
Identify Short Peptides in Proteins
Identify Point Mutations in Proteins
Generate Phylogenetic Tree
Visualize Aligned Sequences
Annotate Nucleotide Sequences
Analyze Sequence Variation (SNP)
Metadata Sequence Analysis
Sequence Format Conversion
Pandemic H1N1 Classification
PCR Primer Design
HISTORY
Retrieve an Analysis
Retrieve a Download
Retrieve an Annotation
Your Analysis History
About Us Community Announcements Links Resources Support Sign Out
You are logged in as [email protected]
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 under Contract No. HHSN266200400041C and is a collaboration between Northrop Grumman Health IT, J. Craig Venter Institute, Vecna Technologies, SAGE Analytica and Los Alamos National Laboratory. University of Texas Southwestern Medical Center was a past subcontractor. Questions, suggestions? Contact us at [email protected]
II. Calculate consensus sequence/sequence variation for your custom sequence set Option 1. Input sequences from search results
1
2.1
Three options to input sequences
Option 2. Use your own custom sequences
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 format.
Paste sequence in FASTADefline in your FASTA file will be used to label the display
Use working set.
Choose a Working Set
TREE GENERATION
Quick Tree (Let IRD set all parameters - view all parameters) Custom Tree (I want to set my own parameters)
SEQUENCE TYPE *
Nucleotide Amino Acid (Protein)
SOURCE OF SEQUENCES TO BE ANALYZED Sequences can also be selected from workbench.
LABELINGDefline in your FASTA file will be used to label the display
FORMAT OF SEQUENCES PROVIDED
Unaligned FASTA Aligned FASTA Phylip (interleaved)
Build TreeClear
Generate Phylogenetic Tree IRD uses PhyML [ Guindon, S. and Gascuel, O., (2003) Syst Biol. 52: 696-704 ] to infer phylogenies based on nucleotide sequences. Additionally, IRD provides severaloptions to display a generated tree. (SOP)Note: An asterisk (*) = required field
Home Generate Phylogenetic Tree
SEARCH DATA ANALYZE & VISUALIZE WORKBENCH SUBMIT DATA HOME
About Us Community Announcements Links Resources Support Sign Out
You are logged in as [email protected]
Cancel Select
Choose Working Set
Name Type Number of Sequences Date
Australia HA 07 & 09 Segment 36 06/03/2011 6:40 PM
california swine flu Segment 4 05/31/2011 2:21 PM
H1N1 NA South Africa Segment 14 05/06/2011 5:49 PM
Perth-HA Segment 14 07/15/2011 1:34 PM
WHO vaccine strains - HA Segment 12 05/31/2011 3:45 PM
Inuenza Research Database - Phylogenetic Tree http://www.udb.org/brc/tree.do?method=ShowCleanInputPage&...
1 of 1 7/29/11 10:01 AM
2.3
1. Search for nucleotide or protein sequences in IRD by using one of the “Search Sequences” options available from the “Search Data” tab.
2. On the search results page, select the desired sequences, mouse-over the “Run Analysis” button and click “Analyze Sequence Variation (SNP)”.
3. Click “Run” on the next page. 4. A Sequence Variation Analysis report will be displayed. Refer to step 3
on the reverse side for explanation of the results.
2
2
3
1. Mouse-over the “Analyze & Visualize” tab and click “Analyze Sequence Variation (SNP)”.
2. On the tool landing page, select “New analysis of sequences you select from the IRD database or upload” in search type. Use one of the three options to input sequences:
2.1 Upload a sequence file in FASTA format OR 2.2 Paste sequences in FASTA format OR 2.3 Use a working set from your Workbench. Then click “Run” to run the analysis. 3. A Sequence Variation Analysis report will be
displayed. Refer to step 3 on the reverse side for explanation of the results.
1
2.2
Select sequences and add them to a working set for future analysis. You’ll need to register a Workbench account
to use this feature.
Click to view details of
the record