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Protocols

Identitag specifications

Information


Unique identifier OMICS_21580
Name Identitag
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download
User data submission Not allowed
Maintained Yes

Maintainers


  • person_outline Laurent Duret
  • person_outline Céline Keime
  • person_outline Olivier Gandrillon
  • person_outline Francesca Damiola
  • person_outline Dominique Mouchiroud

Publication for Identitag

Identitag citations

 (4)
library_books

In Depth Global Analysis of Transcript Abundance Levels in Porcine Alveolar Macrophages Following Infection with Porcine Reproductive and Respiratory Syndrome Virus

2011
PMCID: 3275998
PMID: 22331987
DOI: 10.1155/2010/864181

[…] ags were mapped to transcripts and genes by exact regular expression matching to sequences in GenBank, Harvard Gene Index, and the Pig Expression Database (Japan) databases and parsed into a modified Identitag database []. Multidimensional statistical tests: Audic and Claverie pairwise test; the Fisher's exact test; Greller and Tobin test; the R test and pairwise and general Chi-square tests [] we […]

call_split

Gene expression profiling via LongSAGE in a non model plant species: a case study in seeds of Brassica napus

2009
BMC Genomics
PMCID: 2719671
PMID: 19575793
DOI: 10.1186/1471-2164-10-295
call_split See protocol

[…] t parameters were removed from the analysis. The remaining 834,732 ESTs from NCBI and PBI were annotated based on the alignment with the A. thaliana proteome and orientated in sense using ReadSeq []. Identitag perl scripts were modified so that virtual tags from all positions were extracted from the Brassica ESTs, and the modified Identitag perl scripts were used to create a MySQL database of virt […]

library_books

Large scale analysis by SAGE reveals new mechanisms of v erbA oncogene action

2007
BMC Genomics
PMCID: 2194726
PMID: 17961265
DOI: 10.1186/1471-2164-8-390

[…] the sequencing errors in concatemer sequences (estimated by the Phred quality score for each base), by using the modelling described in Beissbarth et al., 2004.Tag identification was performed using Identitag [] and chicken transcript sequences from the TIGR Gene Index release 10 and from the Refseq databank.In order to assess the significance of the differential expression of tags between the tw […]

library_books

SAGE2Splice: Unmapped SAGE Tags Reveal Novel Splice Junctions

2006
PLoS Comput Biol
PMCID: 1447652
PMID: 16683015
DOI: 10.1371/journal.pcbi.0020034

[…] to genes, including SAGEmap from the National Center for Biotechnology Information (NCBI) [], the National Institutes of Health Cancer Genome Anatomy Project's SAGE Genie [], the Mouse SAGE Site [], Identitag [], and DiscoverySpace []. Despite these efforts, however, a major problem of tag-to-gene mapping exists as approximately one third of the tags are unmapped. Inability to map tags limits the […]

Citations

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Identitag institution(s)
Équipe Signalisation et identités cellulaires, Centre de Génétique Moléculaire et Cellulaire CNRS UMR 5534, Université Claude Bernard Lyon 1, Villeurbanne, France; Équipe Bioinformatique et génomique évolutive, Laboratoire Biométrie et Biologie Évolutive CNRS UMR 5558, Université Claude Bernard Lyon 1, Villeurbanne, France
Identitag funding source(s)
Supported by CNRS, UCBL, INRA (Program "AGENA"), Région Rhône-Alpes (Program "Cellules souches"), Fondation de France, Association pour la Recherche contre le Cancer and a joint INSERM/AFM program (Program "Cellules souches"), by an InterEPST program ("Séquençage à grande échelle", call 2002) and by the EU RTN program "Hematopoiesis" (contract HPRN-CT-2000-00083).

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