Warning: Undefined array key "mm" in /www/wwwroot/www.ai-bt.com/si.php on line 10 Deprecated: trim(): Passing null to parameter #1 ($string) of type string is deprecated in /www/wwwroot/www.ai-bt.com/si.php on line 10 The Iccare web server: an attempt to merge sequence and mapping information for plant and animal species.

Literature DB >> 15215424

The Iccare web server: an attempt to merge sequence and mapping information for plant and animal species.

Cédric Muller¹, Mathieu Denis, Laurent Gentzbittel, Thomas Faraut.

Abstract

The Iccare web server, http://genopole.toulouse.inra.fr/bioinfo/Iccare, provides a simple yet efficient tool for crude EST (expressed sequence tag) annotation specifically dedicated to comparative mapping approaches. Iccare uses all the EST and mRNA sequences from public databases for an organism of interest (query species) and compares them to all the transcripts of one reference organism (Homo sapiens or Arabidopsis thaliana). The results are displayed according to the location of the genes on the chromosomes of the reference organism. Gene structure information and sequence similarities are combined in a graphical representation in order to pinpoint the nature of the transcript query sequence. The user can subsequently design primers or probes for the purpose of physical or genetic mapping. In addition to the query organisms already available in Iccare, users can perform a tailor-made search with their own sequences against the animal or plant reference organism genes.

Entities: Species

Mesh：

Substances：

Year: 2004 PMID： 15215424 PMCID： PMC441598 DOI： 10.1093/nar/gkh460

Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971

51 in total

1. Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.

Authors: A Theologis; J R Ecker; C J Palm; N A Federspiel; S Kaul; O White; J Alonso; H Altafi; R Araujo; C L Bowman; S Y Brooks; E Buehler; A Chan; Q Chao; H Chen; R F Cheuk; C W Chin; M K Chung; L Conn; A B Conway; A R Conway; T H Creasy; K Dewar; P Dunn; P Etgu; T V Feldblyum; J Feng; B Fong; C Y Fujii; J E Gill; A D Goldsmith; B Haas; N F Hansen; B Hughes; L Huizar; J L Hunter; J Jenkins; C Johnson-Hopson; S Khan; E Khaykin; C J Kim; H L Koo; I Kremenetskaia; D B Kurtz; A Kwan; B Lam; S Langin-Hooper; A Lee; J M Lee; C A Lenz; J H Li; Y Li; X Lin; S X Liu; Z A Liu; J S Luros; R Maiti; A Marziali; J Militscher; M Miranda; M Nguyen; W C Nierman; B I Osborne; G Pai; J Peterson; P K Pham; M Rizzo; T Rooney; D Rowley; H Sakano; S L Salzberg; J R Schwartz; P Shinn; A M Southwick; H Sun; L J Tallon; G Tambunga; M J Toriumi; C D Town; T Utterback; S Van Aken; M Vaysberg; V S Vysotskaia; M Walker; D Wu; G Yu; C M Fraser; J C Venter; R W Davis
Journal: Nature Date: 2000-12-14 Impact factor: 49.962

2. High gene density is conserved at syntenic loci of small and large grass genomes.

Authors: C Feuillet; B Keller
Journal: Proc Natl Acad Sci U S A Date: 1999-07-06 Impact factor: 11.205

3. EMBOSS: the European Molecular Biology Open Software Suite.

Authors: P Rice; I Longden; A Bleasby
Journal: Trends Genet Date: 2000-06 Impact factor: 11.639

4. The DNA sequence of human chromosome 21.

Authors: M Hattori; A Fujiyama; T D Taylor; H Watanabe; T Yada; H S Park; A Toyoda; K Ishii; Y Totoki; D K Choi; Y Groner; E Soeda; M Ohki; T Takagi; Y Sakaki; S Taudien; K Blechschmidt; A Polley; U Menzel; J Delabar; K Kumpf; R Lehmann; D Patterson; K Reichwald; A Rump; M Schillhabel; A Schudy; W Zimmermann; A Rosenthal; J Kudoh; K Schibuya; K Kawasaki; S Asakawa; A Shintani; T Sasaki; K Nagamine; S Mitsuyama; S E Antonarakis; S Minoshima; N Shimizu; G Nordsiek; K Hornischer; P Brant; M Scharfe; O Schon; A Desario; J Reichelt; G Kauer; H Blocker; J Ramser; A Beck; S Klages; S Hennig; L Riesselmann; E Dagand; T Haaf; S Wehrmeyer; K Borzym; K Gardiner; D Nizetic; F Francis; H Lehrach; R Reinhardt; M L Yaspo
Journal: Nature Date: 2000-05-18 Impact factor: 49.962

5. Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.

Authors: K Mayer; C Schüller; R Wambutt; G Murphy; G Volckaert; T Pohl; A Düsterhöft; W Stiekema; K D Entian; N Terryn; B Harris; W Ansorge; P Brandt; L Grivell; M Rieger; M Weichselgartner; V de Simone; B Obermaier; R Mache; M Müller; M Kreis; M Delseny; P Puigdomenech; M Watson; T Schmidtheini; B Reichert; D Portatelle; M Perez-Alonso; M Boutry; I Bancroft; P Vos; J Hoheisel; W Zimmermann; H Wedler; P Ridley; S A Langham; B McCullagh; L Bilham; J Robben; J Van der Schueren; B Grymonprez; Y J Chuang; F Vandenbussche; M Braeken; I Weltjens; M Voet; I Bastiaens; R Aert; E Defoor; T Weitzenegger; G Bothe; U Ramsperger; H Hilbert; M Braun; E Holzer; A Brandt; S Peters; M van Staveren; W Dirske; P Mooijman; R Klein Lankhorst; M Rose; J Hauf; P Kötter; S Berneiser; S Hempel; M Feldpausch; S Lamberth; H Van den Daele; A De Keyser; C Buysshaert; J Gielen; R Villarroel; R De Clercq; M Van Montagu; J Rogers; A Cronin; M Quail; S Bray-Allen; L Clark; J Doggett; S Hall; M Kay; N Lennard; K McLay; R Mayes; A Pettett; M A Rajandream; M Lyne; V Benes; S Rechmann; D Borkova; H Blöcker; M Scharfe; M Grimm; T H Löhnert; S Dose; M de Haan; A Maarse; M Schäfer; S Müller-Auer; C Gabel; M Fuchs; B Fartmann; K Granderath; D Dauner; A Herzl; S Neumann; A Argiriou; D Vitale; R Liguori; E Piravandi; O Massenet; F Quigley; G Clabauld; A Mündlein; R Felber; S Schnabl; R Hiller; W Schmidt; A Lecharny; S Aubourg; F Chefdor; R Cooke; C Berger; A Montfort; E Casacuberta; T Gibbons; N Weber; M Vandenbol; M Bargues; J Terol; A Torres; A Perez-Perez; B Purnelle; E Bent; S Johnson; D Tacon; T Jesse; L Heijnen; S Schwarz; P Scholler; S Heber; P Francs; C Bielke; D Frishman; D Haase; K Lemcke; H W Mewes; S Stocker; P Zaccaria; M Bevan; R K Wilson; M de la Bastide; K Habermann; L Parnell; N Dedhia; L Gnoj; K Schutz; E Huang; L Spiegel; M Sehkon; J Murray; P Sheet; M Cordes; J Abu-Threideh; T Stoneking; J Kalicki; T Graves; G Harmon; J Edwards; P Latreille; L Courtney; J Cloud; A Abbott; K Scott; D Johnson; P Minx; D Bentley; B Fulton; N Miller; T Greco; K Kemp; J Kramer; L Fulton; E Mardis; M Dante; K Pepin; L Hillier; J Nelson; J Spieth; E Ryan; S Andrews; C Geisel; D Layman; H Du; J Ali; A Berghoff; K Jones; K Drone; M Cotton; C Joshu; B Antonoiu; M Zidanic; C Strong; H Sun; B Lamar; C Yordan; P Ma; J Zhong; R Preston; D Vil; M Shekher; A Matero; R Shah; I K Swaby; A O'Shaughnessy; M Rodriguez; J Hoffmann; S Till; S Granat; N Shohdy; A Hasegawa; A Hameed; M Lodhi; A Johnson; E Chen; M Marra; R Martienssen; W R McCombie
Journal: Nature Date: 1999-12-16 Impact factor: 49.962

6. Comparing sequenced segments of the tomato and Arabidopsis genomes: large-scale duplication followed by selective gene loss creates a network of synteny.

Authors: H M Ku; T Vision; J Liu; S D Tanksley
Journal: Proc Natl Acad Sci U S A Date: 2000-08-01 Impact factor: 11.205

7. Comparative physical mapping of segments of the genome of Brassica oleracea var. alboglabra that are homoeologous to sequenced regions of chromosomes 4 and 5 of Arabidopsis thaliana.

Authors: C M O'Neill; I Bancroft
Journal: Plant J Date: 2000-07 Impact factor: 6.417

8. Comparative genome analysis reveals extensive conservation of genome organisation for Arabidopsis thaliana and Capsella rubella.

Authors: A Acarkan; M Rossberg; M Koch; R Schmidt
Journal: Plant J Date: 2000-07 Impact factor: 6.417

Review 9. Insights into the structural and functional evolution of plant genomes afforded by the nucleotide sequences of chromosomes 2 and 4 of Arabidopsis thaliana.

Authors: I Bancroft
Journal: Yeast Date: 2000-04 Impact factor: 3.239

10. Estimation of synteny conservation and genome compaction between pufferfish (Fugu) and human.

Authors: A McLysaght; A J Enright; L Skrabanek; K H Wolfe
Journal: Yeast Date: 2000-04 Impact factor: 3.239

11 in total

1. Gene expression profiling in equine polysaccharide storage myopathy revealed inflammation, glycogenesis inhibition, hypoxia and mitochondrial dysfunctions.

Authors: Eric Barrey; Elodie Mucher; Nicolas Jeansoule; Thibaut Larcher; Lydie Guigand; Bérénice Herszberg; Stéphane Chaffaux; Gérard Guérin; Xavier Mata; Philippe Benech; Marielle Canale; Olivier Alibert; Péguy Maltere; Xavier Gidrol
Journal: BMC Vet Res Date: 2009-08-07 Impact factor: 2.741

2. Integrative mapping analysis of chicken microchromosome 16 organization.

Authors: Romain Solinhac; Sophie Leroux; Svetlana Galkina; Olympe Chazara; Katia Feve; Florence Vignoles; Mireille Morisson; Svetlana Derjusheva; Bertrand Bed'hom; Alain Vignal; Valérie Fillon; Frédérique Pitel
Journal: BMC Genomics Date: 2010-11-04 Impact factor: 3.969

3. Transcriptome profiling of sheep granulosa cells and oocytes during early follicular development obtained by laser capture microdissection.

Authors: Agnes Bonnet; Claudia Bevilacqua; Francis Benne; Loys Bodin; Corinne Cotinot; Laurence Liaubet; Magali Sancristobal; Julien Sarry; Elena Terenina; Patrice Martin; Gwenola Tosser-Klopp; Beatrice Mandon-Pepin
Journal: BMC Genomics Date: 2011-08-18 Impact factor: 3.969

4. Phytome: a platform for plant comparative genomics.

Authors: Stefanie Hartmann; Dihui Lu; Jason Phillips; Todd J Vision
Journal: Nucleic Acids Res Date: 2006-01-01 Impact factor: 16.971

5. High resolution physical map of porcine chromosome 7 QTL region and comparative mapping of this region among vertebrate genomes.

Authors: Julie Demars; Juliette Riquet; Katia Feve; Mathieu Gautier; Mireille Morisson; Olivier Demeure; Christine Renard; Patrick Chardon; Denis Milan
Journal: BMC Genomics Date: 2006-01-24 Impact factor: 3.969

6. Integrated maps in quail (Coturnix japonica) confirm the high degree of synteny conservation with chicken (Gallus gallus) despite 35 million years of divergence.

Authors: Boniface B Kayang; Valérie Fillon; Miho Inoue-Murayama; Mitsuru Miwa; Sophie Leroux; Katia Fève; Jean-Louis Monvoisin; Frédérique Pitel; Matthieu Vignoles; Céline Mouilhayrat; Catherine Beaumont; Shin'ichi Ito; Francis Minvielle; Alain Vignal
Journal: BMC Genomics Date: 2006-05-02 Impact factor: 3.969

7. A type I and type II microsatellite linkage map of rainbow trout (Oncorhynchus mykiss) with presumptive coverage of all chromosome arms.

Authors: René Guyomard; Stéphane Mauger; Kamila Tabet-Canale; Sylvain Martineau; Carine Genet; Francine Krieg; Edwige Quillet
Journal: BMC Genomics Date: 2006-11-30 Impact factor: 3.969

8. Construction of a radiation hybrid map of chicken chromosome 2 and alignment to the chicken draft sequence.

Authors: Sophie Leroux; Mélanie Dottax; Suzanne Bardes; Florence Vignoles; Katia Fève; Frédérique Pitel; Mireille Morisson; Alain Vignal
Journal: BMC Genomics Date: 2005-02-04 Impact factor: 3.969

9. Transcriptomic analysis of the dialogue between Pseudorabies virus and porcine epithelial cells during infection.

Authors: Laurence Flori; Claire Rogel-Gaillard; Marielle Cochet; Gaetan Lemonnier; Karine Hugot; Patrick Chardon; Stéphane Robin; François Lefèvre
Journal: BMC Genomics Date: 2008-03-10 Impact factor: 3.969

10. Addition of the microchromosome GGA25 to the chicken genome sequence assembly through radiation hybrid and genetic mapping.

Authors: Marine Douaud; Katia Fève; Marie Gerus; Valérie Fillon; Suzanne Bardes; David Gourichon; Deborah A Dawson; Olivier Hanotte; Terry Burke; Florence Vignoles; Mireille Morisson; Michèle Tixier-Boichard; Alain Vignal; Frédérique Pitel
Journal: BMC Genomics Date: 2008-03-17 Impact factor: 3.969