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Create the page "File Formats" on this wiki! See also the search results found.
- Update the gene '''xfile''': change the name symbol to '''x-file''' and retrieve the changed record. Regenerate the report from Problem 1. T symbol: x-file40 KB (5,672 words) - 21:27, 15 August 2013
- ** db=short symbolic name of datasource (MOD), used to look up conf file ** Sequence feature apps should read/write GenBank & EMBL formats (BioPerl and BioJava handle this). GFF? GTF? BED? GAME? BSML? TIGR add BSML6 KB (985 words) - 05:18, 28 January 2008
- File:Cmap_sample1.jpg File:Cmap_sample2.jpg7 KB (996 words) - 23:40, 17 October 2013
- [[File:Flash gviewer title.jpg|center|Flash GViewer Logo]] ...ckwaveFlash&promoid=BIOW here]. To edit the source code (the <tt>.fla</tt> file in [[SVN]]) and publish modified versions of the <tt>.swf</tt> requires Mac2 KB (339 words) - 19:41, 26 February 2014
- * Annotations can come from a static XML file or can be dynamically generated by a server-side script ...cript that retrieves the data from a database. Details of the various file formats are given below.30 KB (4,819 words) - 21:16, 9 October 2012
- * Supports third party annotation using [[GFF]] formats. ...ns|plug-in]] architecture (e.g. run [[wp:BLAST|BLAST]], dump & import many formats, find oligonucleotides, [[PrimerDesigner.pm|design primers]], create restri11 KB (1,422 words) - 16:47, 10 April 2023
- * DNA files (full chromosomes) in raw and fasta formats * Gene Ontology association file10 KB (1,496 words) - 23:00, 15 August 2013
- | install = See the INSTALL file in the [http://sourceforge.net/projects/gmod/files/blastGraphic/ blastGraph | input = <!-- input formats -->1 KB (188 words) - 18:37, 10 September 2013
- ...from other MODs in terms of data models, user interfaces and data exchange formats. As a result, the research community has to struggle to adjust to new user ...s. Compute interoperability allows software to communicate via shared file formats, transport protocols and database schemas. Both types of interoperability a26 KB (3,975 words) - 05:03, 28 January 2008
- ** flexible configuration of data output formats ...eports and instead expect users to parse information from current, defined formats (which can vary wildly between databases). Some MODs (e.g. FlyMine) allow18 KB (2,786 words) - 17:34, 31 January 2008
- * XORT exchanges data between XML file and database. XORT is generic * GenBank flat-file format to chadoXML converter (Peili Zhang, Chris28 KB (4,338 words) - 22:06, 29 October 2010
- ...|database]]. This does not have to be a relational database; it could be a file or a set of files with or without some kind of index. There's a lot of flex ...e application and translates them to database queries, then receives data, formats it, and sends it back to the application. This piece of software can be tho34 KB (5,526 words) - 19:56, 7 October 2013
- .... In our view these two formats are complementary. Conversions between the formats should be trivial. ...library and follow the instructions in the <code>chaos-xml/INSTALL</code> file.4 KB (647 words) - 21:08, 22 January 2008
- formats. ...The basic state is that users parse information from a given MOD's defined formats (which tend to vary between MODs). Some MODs (e.g. FlyMine, FlyBase) allow24 KB (3,905 words) - 16:54, 11 August 2008
- sh: line 1: ./Build: No such file or directory make images (generates images of the schema in several formats)16 KB (2,472 words) - 23:54, 25 January 2008
- ;<nowiki>Bio::SCF File::Temp</nowiki> io-lib(v1.7+) This will give you a .tar.gz file, which must be uncompressed and unpacked. Then run the following commands35 KB (5,565 words) - 22:39, 8 August 2012
- ...e organism-specific webstart build of Apollo and an accompanying ant build file for repeating the build. ** Chado2Wiki worked via dumps to intermediate flatfile formats11 KB (1,683 words) - 19:54, 9 June 2010
- ...omputer parsable data URL, with no guesswork on spelling, and defined data formats. | Returns a FASTA file containing big DNA fragments (e.g. chromosomes). MIME type is application/x4 KB (607 words) - 22:44, 15 September 2009
- ...f hashes: Bio::SeqFeature::Slim. This is 70% faster for reading a [[GFF]] file. Bio::Feature::IO only supports [[GFF3]]. It is slow, uses heavy objects, * Couple XML response to URL request formats.28 KB (4,093 words) - 05:54, 5 January 2011
- ...and analyses. The customers generally have genome data in hand, in common formats of which Fasta (sequence) and [[GFF]] (annotation) are most common. Custom ...LuceGene Lucegene] : Bio-data indexer that understands various genome data formats, now in use for grid data splitting. Lucene/Lucegene are in java. Advantan7 KB (1,032 words) - 22:42, 15 September 2009
- N-Browse version 2 can save/export data in a variety of formats. Please visit [http://www.gnetbrowse.org N-Browse] for more information. === N-Browse Version 1 Source Code Download (tar.gz file) ===6 KB (920 words) - 16:57, 30 September 2010
- [[File:InterMineLogo.png|link=http://www.intermine.org/wiki/NowHiring|180px|right| ...a warehouses of biological data. It can integrate data from many different formats into a central database and makes the data available to query via a flexibl1 KB (188 words) - 23:12, 9 October 2012
- [[File:InterMineLogo.png|link=http://www.biomed.cam.ac.uk/gradschool/skills/interm ...e] for examples. InterMine can integrate data from many common biological formats and is easy to extend to include your own data. Parsers are included to loa2 KB (283 words) - 23:12, 9 October 2012
- ...after the initial hurdles of learning about configuration options and file formats are overcome. This talk is intended to introduce the more advanced features2 KB (301 words) - 19:41, 18 October 2019
- [[File:web_apollo_demo_login_page_with_credentials_2014.jpg|WebApollo login page|c [[File:web_apollo_select_refseq_2014.jpg|WebApollo reference sequence selection|ce77 KB (11,812 words) - 00:39, 21 May 2014
- ...[GFF]]''' is a standard file format for storing genomic features in a text file. GFF stands for '''''G'''eneric '''F'''eature '''F'''ormat''. GFF files a ...to as GFF2.5. GTF is not a supported format in GMOD so if you have a GTF file you'll need to convert it to [[#GFF3|GFF3]].14 KB (2,081 words) - 02:50, 14 March 2014
- <div class="guideline">When uploading a file, please give the file a meaningful '''Destination filename'''.</div> ...n the file is. Therefore the filename should describe the contents of the file.16 KB (2,420 words) - 23:18, 8 November 2013
- [[File:Das_logo_64x64.jpg|right|link=http://www.biodas.org/|Distributed Annotation * Couple XML response to URL request formats.2 KB (224 words) - 18:47, 17 September 2012
- | [http://genome.ucsc.edu/FAQ/FAQformat.html UCSC Formats] | [http://genome.ucsc.edu/FAQ/FAQformat.html UCSC Formats]3 KB (443 words) - 16:22, 7 August 2012
- ; [[CMapDumper.pm]] : Dumps a tab delimited file that can be read by CMap. ; [[ProteinDumper.pm]] : Dumps translated protein sequences in various formats.2 KB (320 words) - 17:00, 4 December 2012
- <br>[[File:Aug2009MeetingPhoto.JPG|August 2009 GMOD Meeting]] | [[File:GMOD2009Europe300.png|link=GMOD Europe 2009|GMOD Europe 2009]]59 KB (8,741 words) - 19:37, 4 September 2013
- ...ata. After loading, access and rendered performace is equal for all three formats. * Some aspects of the data display can be controlled in the wiggle file15 KB (2,251 words) - 21:22, 25 April 2013
- [[File:Aug2009MeetingPhoto.JPG|link=August 2009 GMOD Meeting|right|August 2009 GMO ...Sequence alignment/map format (SAM) and SAMtools|SAM and SAMtools]]: file formats and programs for compact representation of [[Next Generation Sequencing]] d2 KB (301 words) - 19:37, 4 September 2013
- | [[File:Paglogo.gif|link=http://www.intl-pag.org/|PAG 2009]] * download the zip file and double-click to unpack3 KB (431 words) - 19:34, 3 October 2012
- | valign="center" |[[File:SanDiegoConvention.gif|link=http://www.sandiego.org/nav/Visitors|San Diego [[File:Jan2009Meeting.JPG|center|Jan 2009 Meeting]]50 KB (7,612 words) - 18:53, 8 October 2012
- The sample below is in CLUSTALW format. Other formats are also supported (see below). ==Note on formats==7 KB (897 words) - 21:27, 14 August 2012
- '''GFF''' is a standard file format for storing genomic features in a text file. GFF stands for ''Generic Feature Format''. GFF files are plain text, 9 c Finally, ''[[#GTF|GTF]]'' is another file format that is very similar to GFF and is sometimes referred to as GFF2.5.16 KB (2,336 words) - 19:49, 10 September 2012
- '''GFF''' is a standard file format for storing genomic features in a text file. GFF stands for ''Generic Feature Format''. GFF files are plain text, 9 c Finally, ''[[#GTF|GTF]]'' is another file format that is very similar to GFF and is sometimes referred to as GFF2.5.16 KB (2,387 words) - 22:13, 11 February 2014
- [http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml GFF2] is a supported format in GMOD, '''but it is now de The GFF file format stands for "Gene Finding Format" or or "General Feature Format" and17 KB (2,719 words) - 13:27, 21 April 2017
- ...ls.sourceforge.net SAMtools], a platform agnostic set of programs and file formats for efficiently storing and retrieving short read data.3 KB (450 words) - 00:52, 18 November 2010
- | [[File:Ba2009.png|450px|link=http://www.ausbiotech2009.com.au/bia/bia-home|Bioinfo : The presentation slides are available in two formats. The PowerPoint contains a few useful animations.4 KB (456 words) - 18:52, 8 October 2012
- [[File:Jbrowse_arch.png|600px]] Starting config file:9 KB (1,327 words) - 22:46, 3 October 2012
- ...after the initial hurdles of learning about configuration options and file formats are overcome. This class is intended to help them over those hurdles. * The Data File2 KB (328 words) - 18:52, 8 October 2012
- [[File:ApolloLogo.png|thumb|180px|[[Apollo]]'s new logo, designed by [[Spring 2010 [[File:RedFlyLogo.png|thumb|150px|[http://redfly.ccr.buffalo.edu/ REDFly's] new lo4 KB (668 words) - 01:33, 15 September 2012
- ...alignment database from a multiple sequence alignment file. A variety of formats are supported, including [http://www.bioperl.org/wiki/FASTA_multiple_alignm ...enome alignments but a number of other applications can emit or read these formats.6 KB (931 words) - 22:39, 21 February 2013
- ===The alignment data file=== ...used to process these data will recognize clustalw and other commonly used formats recognized by BioPerl's [http://search.cpan.org/~birney/bioperl-1.2.3/Bio/A19 KB (2,507 words) - 18:53, 8 October 2012
- | [[File:ABRF2010Header.jpg|center|600px|link=http://www.abrf2010.org/|ABRF 2010]] ...that the browser knows about. Make sure that the first column of your GFF file says NC_003070.917 KB (2,763 words) - 18:52, 8 October 2012
- | rowspan="2" | [[File:GMOD2010Europe300.png|center|220px]] [[File:Sept2010MtgLogo300.png|150px|link=September 2010 GMOD Meeting|September 20110 KB (1,367 words) - 17:04, 2 April 2013
- | rowspan="1" | [[File:Sept2010MtgLogo300.png|250px|center]] ...MOD Meeting</b><br />13-14 September 2010<br />Cambridge, UK <br /><br />[[File:Sept2010Group.jpg|center]]100 KB (14,725 words) - 17:31, 30 November 2012
- There are, as yet, no standard flat file formats or loading scripts to load data into this module. Custom scripts will need30 KB (4,604 words) - 16:35, 30 January 2013
