{"type":"doc","content":[{"type":"extension","attrs":{"extensionType":"com.atlassian.confluence.macro.core","extensionKey":"include","parameters":{"macroParams":{"":{"value":"docs:_DE_archived_apps_blurb"}},"macroMetadata":{"schemaVersion":{"value":"1"},"title":"Include Page"}}}},{"type":"heading","attrs":{"level":2},"content":[{"text":"The master copies of EMBOSS documentation are available at ","type":"text"},{"text":"http://emboss.open-bio.org/wiki/Appdocs","type":"text","marks":[{"type":"link","attrs":{"href":"http://emboss.open-bio.org/wiki/Appdocs"}}]},{"text":" on the EMBOSS Wiki.","type":"text"}]},{"type":"paragraph","content":[{"text":" ","type":"text"}]},{"type":"paragraph","content":[{"text":" ","type":"text"},{"type":"inlineExtension","attrs":{"extensionType":"com.atlassian.confluence.migration","extensionKey":"__confluenceADFMigrationUnsupportedContentInternalExtension__","text":"","parameters":{"nestedContent":{"type":"doc","content":[{"type":"bodiedExtension","attrs":{"extensionType":"com.atlassian.confluence.macro.core","extensionKey":"show-if","parameters":{"macroParams":{"atlassian-macro-output-type":{"value":"INLINE"},"group":{"value":"Staff"}},"macroMetadata":{"schemaVersion":{"value":"1"},"title":"show-if"}}},"content":[{"type":"table","attrs":{"layout":"default"},"content":[{"type":"tableRow","content":[{"type":"tableHeader","attrs":{"colspan":1,"background":"Orange","rowspan":1},"content":[{"type":"paragraph","content":[{"text":"VISIBLE ONLY TO STAFF - CONTENT HIDDEN FOR DEPRECATED APP","type":"text","marks":[{"type":"strong"}]}]}]}]},{"type":"tableRow","content":[{"type":"tableCell","attrs":{"colspan":1,"background":"Gainsboro","rowspan":1},"content":[{"type":"heading","attrs":{"level":2},"content":[{"text":"EMBOSS einverted","type":"text"}]},{"type":"paragraph","content":[{"text":"einverted","type":"text","marks":[{"type":"strong"}]},{"text":" finds inverted repeats (stem loops) in nucleotide sequences. It identifies regions of local alignment of the input sequence and its reverse complement that exceed a threshold score. The alignments may include a proportion of mismatches and gaps, which correspond to bulges in the stem loop.","type":"text"}]},{"type":"heading","attrs":{"level":2},"content":[{"text":"Quick Start","type":"text"}]},{"type":"paragraph","content":[{"text":"To use einverted,","type":"text"}]},{"type":"orderedList","attrs":{"order":1},"content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"upload your input sequence data in most format, such as fasta, GenBank, Embl, or Emsembl, gcg formats.","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"choose Application Options of Penalty and Scores","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"launch your job","type":"text"}]}]}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Resource: More information on input sequence feature and format could be found at ","type":"text"},{"text":"https://pods.iplantcollaborative.org/wiki/display/sciplant/EMBOSS+Sequence+Feature+Format","type":"text","marks":[{"type":"link","attrs":{"href":"https://pods.iplantcollaborative.org/wiki/display/sciplant/EMBOSS+Sequence+Feature+Format"}}]}]}]}]},{"type":"heading","attrs":{"level":2},"content":[{"text":"Test Data","type":"text"}]},{"type":"heading","attrs":{"level":4},"content":[{"text":"Input File","type":"text"}]},{"type":"paragraph","content":[{"text":"The input is a standard EMBOSS sequence query (also known as a 'USA', Uniform Sequence Address) with associated feature information, such as GenBank, Embl, and Ensembl formats.","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Test input in GenBank sequence format: Community Data -> iplantcollaborative -> example_data ->EMBOSS -> ","type":"text"},{"text":"Input -> D00596","type":"text","marks":[{"type":"em"}]}]}]}]},{"type":"heading","attrs":{"level":4},"content":[{"text":"Parameters Used in App","type":"text"}]},{"type":"paragraph","content":[{"text":"When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Default parameters only, no further configuration needed.","type":"text"}]}]}]},{"type":"heading","attrs":{"level":4},"content":[{"text":"Output File(s)","type":"text"}]},{"type":"paragraph","content":[{"text":"Standard EMBOSS output sequence file.","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Expected output files: ","type":"text"},{"text":"Community Data -> iplantcollaborative -> example_data ->","type":"text","marks":[{"type":"em"}]},{"text":" ","type":"text"},{"text":"EMBOSS -> Output -> einverted.report and einverted.output","type":"text","marks":[{"type":"em"}]}]}]}]},{"type":"heading","attrs":{"level":2},"content":[{"text":"Tool Source","type":"text"}]},{"type":"paragraph","content":[{"text":"http://emboss.sourceforge.net/apps/cvs/emboss/apps/einverted.html","type":"text","marks":[{"type":"link","attrs":{"href":"http://emboss.sourceforge.net/apps/cvs/emboss/apps/einverted.html"}}]}]}]}]}]}]}],"version":1},"cxhtml":"INLINEStaff

GainsboroOrangeVISIBLE ONLY TO STAFF - CONTENT HIDDEN FOR DEPRECATED APP

EMBOSS einverted

einverted finds inverted repeats (stem loops) in nucleotide sequences. It identifies regions of local alignment of the input sequence and its reverse complement that exceed a threshold score. The alignments may include a proportion of mismatches and gaps, which correspond to bulges in the stem loop.

Quick Start

To use einverted,

upload your input sequence data in most format, such as fasta, GenBank, Embl, or Emsembl, gcg formats.
choose Application Options of Penalty and Scores
launch your job

Resource: More information on input sequence feature and format could be found at https://pods.iplantcollaborative.org/wiki/display/sciplant/EMBOSS+Sequence+Feature+Format

Test Data

Input File

The input is a standard EMBOSS sequence query (also known as a 'USA', Uniform Sequence Address) with associated feature information, such as GenBank, Embl, and Ensembl formats.

Test input in GenBank sequence format: Community Data -> iplantcollaborative -> example_data ->EMBOSS -> Input -> D00596

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.

Default parameters only, no further configuration needed.

Output File(s)

Standard EMBOSS output sequence file.

Expected output files: Community Data -> iplantcollaborative -> example_data -> EMBOSS -> Output -> einverted.report and einverted.output

Tool Source

http://emboss.sourceforge.net/apps/cvs/emboss/apps/einverted.html

"}}}]}],"version":1}

EMBOSS Einverted (archived)

The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.