Pack: Extract Gene Sequence Information with Kepler

Created: 2011-10-05 04:58:33 Last updated: 2011-10-05 06:11:56

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Title: Extract Gene Sequence Information with Kepler

Description

This workflow and pack were designed for a class project. The Kepler based workflow allows one to extract specific information from a gene sequence by using the accession ID as input. By using two web services created for the DNA Data Bank of Japan (DDBJ, http://www.xml.nig.ac.jp/wabi/Method?serviceName=DDBJ&mode=methodList&lang=en), one can extract the sequence header information as an output file, as well as retrieve the sequence, base pair count, and base pair ratios in one output window within Kepler. DDBJ contains the same sequence information as GenBank, therefore the accession ID input works for each web service.

Items (5)

Workflow: Extract Gene Sequence with Kepler (Wdsnellg)

Kepler Workflow

Added by Wdsnellg ... more than 1 year ago (2011-10-05 05:07:10)

External: Extract Gene Sequence Actor - (https://docs.google.com/leaf?id=0B75FJjlkC37wZGUxOGY3NzQtMjA5MS00ZDEwLWEyZTItOTAwZmY0ZWZlMjNm&hl=en_US)

This is what the "Extract Gene Sequence" actor looks like when opened. By using the string substring, string index of, and string length components, I was able to display only the last part of the sequence (ORIGIN) only.

Added by Wdsnellg ... more than 1 year ago (2011-10-05 05:37:14)

External: Extract Header Information Actor - (https://docs.google.com/leaf?id=0B75FJjlkC37wMzc1YzkxMTgtNzVkOS00OTU1LTk4MTUtZTE1NDZmYzMwZTVm&hl=en_US)

This is what the "Extract Header Information" actor looks like when opened. A string substring and string index component are combined to allow only the information above REFERENCE within the sequence results to show.

Added by Wdsnellg ... more than 1 year ago (2011-10-05 05:31:14)

External: Multiple Tab Output - (https://docs.google.com/document/d/13J3rZA4QhLCqmHpgiRvr6IapXVA2AyvDsQH3m-YPmrk/edit?hl=en_US)

This is what the multiple tab output will look like within Kepler. By using two "Multiple Tab" Displays (BP=Base Pair, sequence= gene sequence), one is able to view both output in one window. I did this because the base pair count and ratio data are a summary of the sequence itself, so it made sense to combine them. For this example, the accession ID U49845 was used as the input.

Added by Wdsnellg ... more than 1 year ago (2011-10-05 05:20:26)

External: Header Information File Writer Output - (https://docs.google.com/document/d/1S8yOJa2EW-kyuEiZXCoRQDdlSrSSRKjE_85KwmiIb5o/edit?hl=en_US)

This is the header information file writer output. Within the workflow, one can configure the "Header Information File Writer" actor to change the file name and assign the file destination. This is what the typical output will look like. The accession ID U49845 was used as input for this example.

Added by Wdsnellg ... more than 1 year ago (2011-10-05 05:14:38)