Search results

Create the page "Briggsae genomic" on this wiki! See also the search results found.

• 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
• WormBase Model:Sequence
  // Stores: genomic DNA objects (chromosomes, superlinks, and clones) ...AGP_parent UNIQUE ?Sequence XREF AGP_fragment // added to hold briggsae data [krb 020726]
  12 KB (1,258 words) - 09:29, 5 October 2010
• FIGURE(S)
  ...heir experimental evidence, and links to DNA and protein sequences, a ''C. briggsae'' ortholog, and external database records. '''(http://www.wormbase.org/wiki/index.php/Image:Fig_1_8_04.png) Genetic and genomic information from the Gene page for ''zyg-1''.''' Further down the same page
  19 KB (3,061 words) - 23:01, 13 August 2010
• Caenorhabditis angaria
  ...t separate from, the more familiar Elegans group containing C. elegans, C. briggsae, C. remanei, and other elegans look-alikes. Meanwhile, the genome of C. ang * [Oct 2010] The genomic sequencing and analysis of C. sp. 3 PS1010 is now
  3 KB (437 words) - 16:02, 15 December 2011
• WS228
  - G_SPECIES.WS228.genomic.fa.gz - Unmasked genomic DNA ...S228.genomic_masked.fa.gz - Hard-masked (repeats replaced with Ns) genomic DNA
  14 KB (1,572 words) - 10:37, 11 November 2011
• WS173
  human, fly, yeast, C. briggsae, and SwissProt &amp; TrEMBL proteins. xii) best_blastp_hits_brigprot.WS173.gz - for each C. briggsae protein, lists Best blastp match to
  6 KB (639 words) - 10:55, 21 December 2011
• WS234
  - G_SPECIES.WS234.genomic.fa.gz - Unmasked genomic DNA ...S234.genomic_masked.fa.gz - Hard-masked (repeats replaced with Ns) genomic DNA
  15 KB (1,653 words) - 10:13, 18 January 2013
• WormBase Newsletter No. 3, October 2003
  The number of predictions annotated onto the genomic sequence has also steadily increased from ~19,000 in the 1998 Science publi === The C. briggsae genome sequence ===
  10 KB (1,509 words) - 15:40, 24 September 2007
• WS235
  - G_SPECIES.WS235.genomic.fa.gz - Unmasked genomic DNA ...S235.genomic_masked.fa.gz - Hard-masked (repeats replaced with Ns) genomic DNA
  15 KB (1,708 words) - 10:14, 18 January 2013
• WS201
  human, fly, yeast, C. briggsae, and SwissProt & TrEMBL proteins. xii) best_blastp_hits_brigprot.WS201.gz - for each C. briggsae protein, lists Best blastp match to
  6 KB (665 words) - 16:42, 21 December 2011
• WS232
  - G_SPECIES.WS232.genomic.fa.gz - Unmasked genomic DNA ...S232.genomic_masked.fa.gz - Hard-masked (repeats replaced with Ns) genomic DNA
  15 KB (1,729 words) - 14:15, 13 September 2012
• WS230
  - G_SPECIES.WS230.genomic.fa.gz - Unmasked genomic DNA ...S230.genomic_masked.fa.gz - Hard-masked (repeats replaced with Ns) genomic DNA
  17 KB (1,950 words) - 09:37, 7 February 2012
• WS146
  human, fly, yeast, C. briggsae, and SwissProt & TrEMBL proteins. xii) best_blastp_hits_brigprot.WS146.gz - for each C. briggsae protein, lists Best blastp match to
  6 KB (670 words) - 11:09, 21 December 2011
• WS227
  - G_SPECIES.WS227.genomic.fa.gz - Unmasked genomic DNA ...S227.genomic_masked.fa.gz - Hard-masked (repeats replaced with Ns) genomic DNA
  15 KB (1,738 words) - 11:20, 21 December 2011
• WS289
  ...- G_SPECIES.BIOPROJECT.WS288.genomic.fa.gz - Unmasked genomic DNA ...88.genomic_masked.fa.gz - Hard-masked (repeats replaced with Ns) genomic DNA
  16 KB (1,733 words) - 21:55, 11 May 2023
• WS182
  human, fly, yeast, C. briggsae, and SwissProt & TrEMBL proteins. xii) best_blastp_hits_brigprot.WS182.gz - for each C. briggsae protein, lists Best blastp match to
  6 KB (716 words) - 16:48, 21 December 2011
• WS231
  - G_SPECIES.WS231.genomic.fa.gz - Unmasked genomic DNA ...S231.genomic_masked.fa.gz - Hard-masked (repeats replaced with Ns) genomic DNA
  16 KB (1,820 words) - 14:15, 13 September 2012
• WS176
  human, fly, yeast, C. briggsae, and SwissProt &amp; TrEMBL proteins. xii) best_blastp_hits_brigprot.WS176.gz - for each C. briggsae protein, lists Best blastp match to
  7 KB (783 words) - 10:46, 21 December 2011
• WS233
  - G_SPECIES.WS233.genomic.fa.gz - Unmasked genomic DNA ...S233.genomic_masked.fa.gz - Hard-masked (repeats replaced with Ns) genomic DNA
  17 KB (2,002 words) - 14:17, 13 September 2012
• WS229
  - G_SPECIES.WS229.genomic.fa.gz - Unmasked genomic DNA ...S229.genomic_masked.fa.gz - Hard-masked (repeats replaced with Ns) genomic DNA
  17 KB (1,988 words) - 11:15, 21 December 2011
• WS206
  human, fly, yeast, C. briggsae, and SwissProt & TrEMBL proteins. xii) best_blastp_hits_brigprot.WS206.gz - for each C. briggsae protein, lists Best blastp match to
  7 KB (796 words) - 16:46, 21 December 2011
• WS284
  ...- G_SPECIES.BIOPROJECT.WS284.genomic.fa.gz - Unmasked genomic DNA ...84.genomic_masked.fa.gz - Hard-masked (repeats replaced with Ns) genomic DNA
  17 KB (1,841 words) - 21:54, 11 May 2023
• WS224
  human, fly, yeast, C. briggsae, and SwissProt & TrEMBL proteins. sequences/dna - WormBase dna data genomic sequence (raw, soft_masked masked), agp
  15 KB (1,583 words) - 11:13, 21 December 2011
• WS222
  human, fly, yeast, C. briggsae, and SwissProt & TrEMBL proteins. sequences/dna - WormBase dna data genomic sequence (raw, soft_masked masked), agp
  15 KB (1,647 words) - 10:06, 22 December 2010
• WS226
  - G_SPECIES.WS226.genomic.fa.gz - Unmasked genomic DNA ...S226.genomic_masked.fa.gz - Hard-masked (repeats replaced with Ns) genomic DNA
  21 KB (2,346 words) - 11:15, 21 December 2011
• WS223
  human, fly, yeast, C. briggsae, and SwissProt & TrEMBL proteins. sequences/dna - WormBase dna data genomic sequence (raw, soft_masked masked), agp
  15 KB (1,610 words) - 11:20, 21 December 2011
• BASIC PROTOCOL 11: DOWNLOADING A BATCH OF SEQUENCES
  ...Genome Dumper can extract data from either the ''C. elegans'' or the ''C. briggsae'' genome. Pick the species to be scanned from the Species menu. ...utomatically translate classical gene names (such as ''zyg-1'') into their genomic sequence equivalents (such as F59E12.2), so translating classical gene list
  4 KB (687 words) - 19:56, 11 August 2010
• WS225
  human, fly, yeast, C. briggsae, and SwissProt & TrEMBL proteins. sequences/dna - WormBase dna data genomic sequence (raw, soft_masked masked), agp
  16 KB (1,674 words) - 11:38, 20 April 2011
• WS221
  human, fly, yeast, C. briggsae, and SwissProt & TrEMBL proteins. sequences/dna - WormBase dna data genomic sequence (raw, soft_masked masked), agp
  17 KB (1,758 words) - 16:47, 21 December 2011
• WS193
  human, fly, yeast, C. briggsae, and SwissProt &amp; TrEMBL proteins. xii) best_blastp_hits_brigprot.WS193.gz - for each C. briggsae protein, lists Best blastp match to
  8 KB (944 words) - 16:52, 21 December 2011
• WS218
  human, fly, yeast, C. briggsae, and SwissProt & TrEMBL proteins. sequences/dna - WormBase dna data genomic sequence (raw, soft_masked
  15 KB (1,756 words) - 11:21, 21 December 2011
• WS219
  human, fly, yeast, C. briggsae, and SwissProt & TrEMBL proteins. sequences/dna - WormBase dna data genomic sequence (raw, soft_masked masked), agp
  15 KB (1,622 words) - 11:11, 21 December 2011
• WS174
  human, fly, yeast, C. briggsae, and SwissProt &amp; TrEMBL proteins. xii) best_blastp_hits_brigprot.WS174.gz - for each C. briggsae protein, lists Best blastp match to
  8 KB (938 words) - 10:54, 21 December 2011
• NGASP
  ...ditis'' genomes to five when added to the existing ''C. elegans'' and ''C. briggsae'' genome sequences. ...As, while 2) a 'full set' will contain all curated genes from the selected genomic regions. This competition differs from the ''Drosophila'' GASP and human EG
  21 KB (3,246 words) - 23:20, 13 August 2010
• Glossary of terms
  ...levels of evolutionary relatedness: groups built solely from C. elegans-C. briggsae ortholog pairs (~13,000 "InP_Cae_*" groups); those built from metazoan orth ...overlapping genes and the corresponding locations are usually the primary genomic targets of an RNAi experiment. Note that it is possible for a probe to have
  8 KB (1,256 words) - 00:26, 31 August 2010
• WS220
  human, fly, yeast, C. briggsae, and SwissProt & TrEMBL proteins. sequences/dna - WormBase dna data genomic sequence (raw, soft_masked masked), agp
  16 KB (1,762 words) - 11:10, 21 December 2011
• WormBase Paper Categorization
  **Genomic classification of protein-coding gene families *Genomic classification of protein-coding gene families
  10 KB (1,279 words) - 18:20, 18 October 2013
• Software Life Cycle: 1. Updating The Development Server
  <td>Load Genomic GFF databases</td> ...c sequence and conceptual translations. In addition, for C. elegans and C. briggsae, we build blast databases for ESTs and "genes" (actually clones).
  25 KB (3,632 words) - 03:11, 28 October 2013
• Virtual Machines
  Bio::DB::GFF - ''Perl API to genomic annotations'' ...es of genomic annotations, including (as of WS170, 2/2007), C. elegans, C. briggsae, and C. remanei. You can use the Bio::DB::GFF API -- part of BioPerl -- to
  11 KB (1,664 words) - 18:43, 17 August 2010
• Journal first-pass (jfp) postgres table details
  ...if data is presented for any species other than ''C. elegans'', e.g., ''C. briggsae'', ''Pristionchus pacificus'', ''Brugia malayi'', etc. || ...names (e.g., sjj_ZK617.1, cenix:155-g4, mv_CAA3346 or the library used), genomic coordinates of the primers (e.g. IV:11970667..12012891, ZK1067:13703..22295
  16 KB (2,310 words) - 11:05, 21 December 2011
• ModENCODE Integration status
  This is a single tiling-array data-set of genomic regions in the 'embryo' life-stage - it looks like a test for a project tha This is a single tiling-array data-set of genomic regions in the 'young adult' life-stage - it looks like a test for a projec
  17 KB (2,478 words) - 14:07, 5 July 2012
• Jfp postgres table details
  ...if data is presented for any species other than ''C. elegans'', e.g., ''C. briggsae'', ''Pristionchus pacificus'', ''Brugia malayi'', etc. || ...names (e.g., sjj_ZK617.1, cenix:155-g4, mv_CAA3346 or the library used), genomic coordinates of the primers (e.g. IV:11970667..12012891, ZK1067:13703..22295
  13 KB (1,960 words) - 11:07, 21 December 2011
• FAQs
  === Where can I get repeatmasked genomic sequences for ''C. elegans'', ''C. briggsae'', or ''C. remanei''? === The ''C. briggsae'' repeatmasked genomic sequence is here, for assembly cb25.agp8:
  67 KB (10,954 words) - 09:22, 19 February 2013
• OA forms, tables, scripts, etc
  ...transgenes_summary.pl transgenes_summary.pl] finds Is/In/Ex transgenes and genomic expressions (not put in any pipeline yet<br><br> /home/citpub/Karen/TgSumm ...hus pacificus<br>Homo sapiens<br>Caenorhabditis japonica<br>Caenorhabditis briggsae<br>Cruznema tripartitum<br>Caenorhabditis sp.3<br>Brugia malayi<br>Caenorha
  20 KB (3,050 words) - 21:01, 19 April 2017
• Project page for author first pass form
  ...if data is presented for any species other than ''C. elegans'', e.g., ''C. briggsae'', ''Pristionchus pacificus'', ''Brugia malayi'', etc. || ...ports PFMs or PWMs, which are typically used to define regulatory sites in genomic DNA (e.g., bound by transcription factors) or mRNA (e.g., bound by translat
  11 KB (1,688 words) - 11:06, 21 December 2011
• Datatypes flagged
  ...C. elegans: ''' Data is presented for Caenorhabditis sister species e.g., briggsae, remanei, and/or related nematodes, parasitic nematodes. Postgres charact ...ports PFMs or PWMs, which are typically used to define regulatory sites in genomic DNA (e.g., bound by transcription factors) or mRNA (e.g., bound by translat
  12 KB (1,832 words) - 18:43, 11 August 2010
• UserGuide:Revised Nomenclature
  ...ually curated.</p><ul><li><i>C. elegans</i><li><i>C. brenneri</i><li><i>C. briggsae</i><li><i>C. japonica</i><li><i>C. remanei</i><li><i>Brugia malayi</i></ul> ...d, being left as various sizes of contig. Only <i>C. elegans</i> and <i>C. briggsae</i> have been assembled into chromosomes.
  56 KB (9,514 words) - 09:48, 23 October 2015
• UserGuide:Reivsed Nomenclature
  ...ually curated.</p><ul><li><i>C. elegans</i><li><i>C. brenneri</i><li><i>C. briggsae</i><li><i>C. japonica</i><li><i>C. remanei</i><li><i>Brugia malayi</i></ul> ...d, being left as various sizes of contig. Only <i>C. elegans</i> and <i>C. briggsae</i> have been assembled into chromosomes.
  56 KB (9,520 words) - 11:51, 21 October 2015
• COMMENTARY
  ...nomic sequence has been aligned to orthologous sites in the genome of ''C. briggsae'', a sibling species of ''C. elegans'' (Stein et al., 2003). Finally, there ...the main site, and be syntenically aligned to the ''C. elegans'' and ''C. briggsae'' genomes.
  30 KB (4,765 words) - 20:03, 11 August 2010
• WormMine
  | 6238 || Caenorhabditis briggsae | Genomic sequences
  15 KB (2,088 words) - 16:16, 15 October 2020
• Updating WormBase
  - calculates genomic coordinates of protein motifs For C. briggsae
  34 KB (5,450 words) - 18:24, 17 August 2010
• Texpresso/Author/Curator interim form
  ...if data is reported for any species other than ''C. elegans'', e.g., ''C. briggsae'', ''Pristionchus pacificus'', ''Brugia malayi'', etc. |||| ...ports PFMs or PWMs, which are typically used to define regulatory sites in genomic DNA (e.g., bound by transcription factors) or mRNA (e.g., bound by translat
  17 KB (2,417 words) - 11:04, 21 December 2011
• Searching WormBase for Information About C. elegans (Wiley)
  ...l connectivity. Also, WormBase contains sequence and gene structures of C. briggsae and C. remanei, two closely related worms. These data are interconnected, s ...Query Language; batch downloads of many sequences at once; identifying the genomic regions, genetic contents, or molecular clones spanning a defined chromosom
  103 KB (16,375 words) - 23:39, 30 November 2010
• WS215
  human, fly, yeast, C. briggsae, and SwissProt & TrEMBL proteins. xii) best_blastp_hits_brigprot.WS215.gz - for each C. briggsae protein, lists Best blastp match to
  19 KB (1,735 words) - 11:07, 21 December 2011
• Unused Attributes
  | :sequence/briggsae-canonical | :sequence/genomic
  35 KB (4,174 words) - 10:52, 2 February 2015
• WS244 Models.wrm
  ...AGP_parent UNIQUE ?Sequence XREF AGP_fragment // added to hold briggsae data [krb 020726] > AGP_parent UNIQUE ?Sequence XREF AGP_fragment // added to hold briggsae data [krb 020726]
  235 KB (23,325 words) - 10:33, 3 July 2014