{"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 checktrans","type":"text"}]},{"type":"paragraph","content":[{"text":"checktrans","type":"text","marks":[{"type":"strong"}]},{"text":" reads a protein sequence containing stop characters and writes a statistical report of any open reading frames (ORFs) that are greater than a minimum size.","type":"text"}]},{"type":"heading","attrs":{"level":2},"content":[{"text":"Quick Start","type":"text"}]},{"type":"paragraph","content":[{"text":"To use ","type":"text"},{"text":"checktrans","type":"text","marks":[{"type":"strong"}]},{"text":",","type":"text"}]},{"type":"orderedList","attrs":{"order":1},"content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"upload your input data in most format, such as fasta, GenBank, Embl, or Emsembl, gcg formats.","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Choose your option, such as reverse","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 can be in most sequence format, such as fasta, gcg, GenBank, Embl, and Ensembl formats. For details, please see ","type":"text"},{"text":"http://emboss.sourceforge.net/apps/release/6.0/emboss/apps/seqret.html","type":"text","marks":[{"type":"link","attrs":{"href":"http://emboss.sourceforge.net/apps/release/6.0/emboss/apps/seqret.html"}}]}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Test input in GenBank sequence format: Community Data -> iplantcollaborative -> example_data ->EMBOSS -> Input -> paamir.pep","type":"text"}]}]}]},{"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, including report file, sequence file, feature files.","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","type":"text","marks":[{"type":"em"}]},{"text":" ","type":"text"},{"text":"->","type":"text","marks":[{"type":"em"}]},{"text":" ","type":"text"},{"text":"checktrans.report, checktrans.fasta, checktrans.gff","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/checktrans.html","type":"text","marks":[{"type":"link","attrs":{"href":"http://emboss.sourceforge.net/apps/cvs/emboss/apps/checktrans.html"}}]}]}]}]}]}]}],"version":1},"cxhtml":"INLINEStaff

GainsboroOrangeVISIBLE ONLY TO STAFF - CONTENT HIDDEN FOR DEPRECATED APP

EMBOSS checktrans

checktrans reads a protein sequence containing stop characters and writes a statistical report of any open reading frames (ORFs) that are greater than a minimum size.

Quick Start

To use checktrans,

upload your input data in most format, such as fasta, GenBank, Embl, or Emsembl, gcg formats.
Choose your option, such as reverse
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 can be in most sequence format, such as fasta, gcg, GenBank, Embl, and Ensembl formats. For details, please see http://emboss.sourceforge.net/apps/release/6.0/emboss/apps/seqret.html

Test input in GenBank sequence format: Community Data -> iplantcollaborative -> example_data ->EMBOSS -> Input -> paamir.pep

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, including report file, sequence file, feature files.

Expected output files: Community Data -> iplantcollaborative -> example_data -> EMBOSS -> Output -> checktrans.report, checktrans.fasta, checktrans.gff

Tool Source

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

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

EMBOSS Checktrans (archived)

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