Hi Karine, if I understand correctly, you want to extract all intronic sequences for all human olfactory receptor genes (GO:0004984).
The first step is to get gene identifiers for GO:0004984, the second step to get their intronic sequences. I am unsure on how to resolve GO to gene identifiers with the UCSC database, so I am using Ensembl Biomart for this. To get all genes for a GO category: Go to www.biomart.org, select Ensembl Genes, Homo sapiens, click filter, click Gene ontology, check GO Term Accession, paste GO:0004984, click Attributes, un-select "Ensemb Gene ID", leave "Ensembl Transcript Id" selected. Click Results, select "View": "All", select Format: "TSV". Copy the list of genes without the first header line. To get all introns of these genes: Go to the UCSC Table Browser, select Homo sapiens, select group: Genes and Gene Prediction Tracks, select track: Ensembl genes, under "identifiers" click "paste list", paste the list of transcript identifiers, click submit, ignore the error message (there is a version difference between UCSC and Ensembl), under "output format" select "sequence", click submit. Select "genomic" coordinates when asked. Select "introns" and deselect all other checkboxes when asked. A last click on submit should give you the sequences in fasta format of all olfactory introns. Don't hesitate to email the list again if you have any other questions. all the best Max ---------- Forwarded message ---------- From: Karine Badonnel <[email protected]> Date: 2011/7/7 Subject: question bioinfo!! To: Maximilian Haussler <[email protected]> Salut Max, Sais-tu comment extraire en bloc tous les introns de chaque récepteur olfactif de rat (~1500, GO:0004984)? Bises. Karine. -- Karine BADONNEL, IR NOeMI Neurobiologie de l'Olfaction et Modélisation en Imagerie, UR1197 Biologie de l'Olfaction et Biosenseurs (BOB) INRA, Bat. Biotechnologies, Domaine de Vilvert F-78350 Jouy-en-Josas, France tel : 01 34 65 24 11 fax : 01 34 65 22 41 http://www.jouy.inra.fr/noemi _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
