IMGT: Difference between revisions
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== Intro == | |||
* Basic problem: If you have an immune receptor sequence, e.g. antibody or T-Cell receptor, how do you call it? | * Basic problem: If you have an immune receptor sequence, e.g. antibody or T-Cell receptor, how do you call it? | ||
* Just like for all other nucleotide sequences: We need | * Just like for all other nucleotide sequences: We need | ||
| Line 5: | Line 6: | ||
** genes (like NCBI Genes) | ** genes (like NCBI Genes) | ||
** and people that sort this whole mess | ** and people that sort this whole mess | ||
== IMGT Structure == | |||
* The main reference database for immune loci is IMGT.org | * The main reference database for immune loci is IMGT.org | ||
* It consists of databases, tools and additional files (e.g. ontology, some notes, etc) | * It consists of databases, tools and additional files (e.g. ontology, some notes, etc) | ||
| Line 25: | Line 27: | ||
*** e.g. [http://www.imgt.org/IMGT_GENE-DB/GENElect?query=2+IGHV1-18&species=Homo+sapiens IGHV1-18] | *** e.g. [http://www.imgt.org/IMGT_GENE-DB/GENElect?query=2+IGHV1-18&species=Homo+sapiens IGHV1-18] | ||
*** <positionOnGenome> starts from one and numbers the genes along the chromosome, see [http://genome.ucsc.edu/cgi-bin/hgTracks?insideX=118&revCmplDisp=0&hgsid=202563483&hgt_doJsCommand=&position=chr14%3A106%2C368%2C424-106%2C388%2C490&hgtgroup_map_close=0&hgtgroup_phenDis_close=1&hgtgroup_genes_close=0&hgtgroup_rna_close=0&hgtgroup_expression_close=0&hgtgroup_regulation_close=0&hgtgroup_compGeno_close=0&hgtgroup_neandertal_close=1&hgtgroup_varRep_close=0 genome browser (switch on encode genes)] | *** <positionOnGenome> starts from one and numbers the genes along the chromosome, see [http://genome.ucsc.edu/cgi-bin/hgTracks?insideX=118&revCmplDisp=0&hgsid=202563483&hgt_doJsCommand=&position=chr14%3A106%2C368%2C424-106%2C388%2C490&hgtgroup_map_close=0&hgtgroup_phenDis_close=1&hgtgroup_genes_close=0&hgtgroup_rna_close=0&hgtgroup_expression_close=0&hgtgroup_regulation_close=0&hgtgroup_compGeno_close=0&hgtgroup_neandertal_close=1&hgtgroup_varRep_close=0 genome browser (switch on encode genes)] | ||
*** [http://www.ncbi.nlm.nih.gov/pubmed/6784929 | *** [http://www.imgt.org/IMGTindex/orphon.html Orphons] [http://www.ncbi.nlm.nih.gov/pubmed/6784929 (old paper)] seem to be (nonfunctional?) copies of receptors on other chromosomes | ||
** Repertoire: descriptions of loci, genes and 3D-structures | ** Repertoire: descriptions of loci, genes and 3D-structures | ||
*** Example human IGH [http://www.imgt.org/textes/IMGTrepertoire/LocusGenes/chromosomes/human/IGH/Hu_IGHchrom14.html] | *** Example human IGH [http://www.imgt.org/textes/IMGTrepertoire/LocusGenes/chromosomes/human/IGH/Hu_IGHchrom14.html] | ||
Revision as of 17:27, 12 July 2011
Intro
- Basic problem: If you have an immune receptor sequence, e.g. antibody or T-Cell receptor, how do you call it?
- Just like for all other nucleotide sequences: We need
- submitted sequences (like Genbank)
- "reference" sequences (like RefSeq)
- genes (like NCBI Genes)
- and people that sort this whole mess
IMGT Structure
- The main reference database for immune loci is IMGT.org
- It consists of databases, tools and additional files (e.g. ontology, some notes, etc)
- LIGM-DB: Nucleotide sequences of all kinds. Can be C, V, J, D, or combinations thereof.
- Seems to be pulling in from Genbank and change their annotations slightly with different keywords
- Automatic transformation or manual annotation?
- Looks like they could have a BLAST-based pipeline that annotates the different fragments
- Annotates Genbank sequences with the CVDJ-numbers
- Example: Genbank AF139844
- in IMGT: http://imgt.org/cgi-bin/IMGTlect.jv?query=201+AF139844
- on NCBI: http://www.ncbi.nlm.nih.gov/nuccore/4732152?report=graph
- Both look very similar, almost identical information
- Annotations that they add: Ftable
- MHC-DB
- GENE-DB: A list of categorized VDJC sequences and all their alleles
- Naming is <locus><type><type>-<positionOnGenome></OrphonIdentifier>*allele
- e.g. IGHV1-18
- <positionOnGenome> starts from one and numbers the genes along the chromosome, see genome browser (switch on encode genes)
- Orphons (old paper) seem to be (nonfunctional?) copies of receptors on other chromosomes
- Repertoire: descriptions of loci, genes and 3D-structures
- Web Resources: A mixed bag with explanations on how they curate
- Actually the best starting point
- LIGM-DB: Nucleotide sequences of all kinds. Can be C, V, J, D, or combinations thereof.
