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• Species available through WormBase (overview)
  |[http://www.wormbase.org/db/searches/blast_blat BLAST Search]<br>genomic, proteins ...ormbase.org/db/searches/blast_blat BLAST Search]<br>genes, proteins, ests, genomic
  5 KB (641 words) - 08:30, 27 September 2010
• Caenorhabditis briggsae
  ''Caenorhabditis briggsae'' is a hermaphroditic species closely related to ''C. elegans'' (i.e., a fe 1. A general [http://www.briggsae.org/ ''C. briggsae'' research page].
  2 KB (312 words) - 15:46, 15 December 2011
• Reagents
  * C. elegans genomic [[Cosmids/YACs]] *C. briggsae genomic clones: [http://bacpac.chori.org/library.php?id=26 information] | [http://b
  2 KB (271 words) - 15:10, 22 September 2021
• INTRODUCTION
  ...connectivity. Also, WormBase contains sequence and gene structures of ''C. briggsae'' and ''C. remanei'', two closely related worms. These data are interconnec ...Query Language; batch downloads of many sequences at once; identifying the genomic regions, genetic contents, or molecular clones spanning a defined chromosom
  2 KB (365 words) - 00:06, 1 December 2010
• Caenorhabditis japonica
  ...cing on account of its providing the best (closest) available outgroup for genomic comparisons with Elegans group members.
  2 KB (264 words) - 16:01, 15 December 2011
• BASIC PROTOCOL 8: VIEWING THE C. BRIGGSAE GENOME AND ITS SYNTENY WITH C. ELEGANS
  ...sae'' genome and a preliminary assembly of the ''C. remanei'' genome. ''C. briggsae'''s genome can be viewed either by itself or in syntenic linkages to ''C. e ...in the same way as with ''C. elegans'' (http://wormbase.org/db/seq/gbrowse/briggsae<nowiki>;). </nowiki>
  4 KB (705 words) - 20:02, 11 August 2010
• Downloads
  == Genomic annotations in GFF format == ...ovides raw annotations for integration into your own local database. These genomic annotations are distributed in the [http://www.sanger.ac.uk/Software/format
  8 KB (1,219 words) - 22:33, 24 October 2011
• Discussion
  #Consider also evaluating pipeline on a small genomic region of ''C. briggsae''. Species-specific differences e.g. hexamer usage in CDS &amp; exon/intron ...could easily produce new blastz alignments (which they have for the old ''briggsae'' non-chromosomal assembly). - ''Avril''
  3 KB (454 words) - 18:54, 11 August 2010
• UserGuide:Sequence Page
  ...exons in the genome, and STSes, SNPs, and transposons that can be used for genomic mapping or site-selected mutagenesis. ...to the Protein page for its gene product (where applicable) and to its C. briggsae ortholog (where one is known to exist). Other data such as the source clone
  3 KB (490 words) - 18:31, 17 August 2010
• UserGuide:Browse Genome
  ...tive traits. You want to extract it directly from Wormbase and analyse its genomic context in detail. Where to go? ...s to a known genomic component, the Genome Browser page will give you that genomic component itself if it has been entered into Wormbase, or make an effort to
  6 KB (975 words) - 18:25, 17 August 2010
• BASIC PROTOCOL 4: EXAMINING A MOLECULAR SEQUENCE IN C. ELEGANS
  ...equence will have diverse information, with a somewhat greater emphasis on genomic sequence rather than classical biology. ...page also gives links to the Protein page for zyg-1/F59E12.2 and to the C. briggsae ortholog of</nowiki>'' zyg-1.
  2 KB (343 words) - 19:57, 11 August 2010
• Mining WormBase with Bio::DB::GFF
  ...provides a simple relational schema and database access layer for querying genomic features. This is the access method of choice to use for mining WormBase fo ...ntron of another gene. Comparing syntenic regions of the C. elegans and C. briggsae genomes. You will need to install your own local database. Currently WormBa
  11 KB (1,663 words) - 17:45, 16 August 2010
• BASIC PROTOCOL 7: USING THE GENOME BROWSER
  ...t biological features reside. WormBase thus provides schematic diagrams of genomic DNA, as well as textual descriptions of genes, with a Generic Genome Browse '''''Study a particular genomic region'''''
  7 KB (1,189 words) - 20:01, 11 August 2010
• WormBaseComparativeGenomicsTools
  = Genomic Alignments = ...alignment). Or in the ACeDB database as Homol_data on the C.elegans and C.briggsae chromosomes.
  5 KB (727 words) - 17:31, 27 June 2009
• ComparaTutorial
  -species =&gt; <span><font color="#ff0000">'Caenorhabditis briggsae'</font></span>,-group =&gt; <span><font color="#ff0000">'core'</font></span = Genomic Alignments =
  21 KB (2,963 words) - 18:18, 11 August 2010
• INDI
  * WBPaper00046462 The recent discovery of a C. briggsae sister species, C. nigoni, has we first generated 96 chromosomally integrated GFP markers in the C. briggsae genome
  3 KB (452 words) - 21:59, 20 March 2015
• UserGuide:Gene Page
  ...phical and text alignments of the corresponding C. elegans and C. briggsae genomic regions (View Synteny). Genomic Position: Links to physical map via genome browser. Display can be customiz
  7 KB (985 words) - 18:28, 17 August 2010
• Data mining:WormMart
  ...of filters to constrain retrieved results. Filters include such things as genomic location and the presence or absence of specific annotations. Data can be r ...mple 2|Example 2]] From all genes in C.elegans that have an ortholog in C. briggsae, are located in chromosome III, are sterile in an RNAi screen, and have ann
  2 KB (275 words) - 10:40, 31 January 2013
• WS183
  human, fly, yeast, C. briggsae, and SwissProt & TrEMBL proteins. xii) best_blastp_hits_brigprot.WS183.gz - for each C. briggsae protein, lists Best blastp match to
  7 KB (800 words) - 10:01, 8 November 2007
• UserGuide:Nomenclature nematode
  Increasing amounts of genomic and genetic information have become available for other nematode species. D ...andard prefix and hyphen can be added to the gene name. Examples: the ''C. briggsae'' and ''Pristionchus pacificus'' orthologs of ''C. elegans tra-1'' are call
  6 KB (977 words) - 19:43, 14 June 2011

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