Hi Steffen, Thanks for the information. Best regards, Simon Steffen at stat.Berkeley.EDU wrote: > Hi Simon, > > The cdna attribute is the combination of 5utr + coding + 3utr so you can > remove 5utr, coding and 3utr from your list of attributes to retrieve. I > would take ensembl_transcript_id instead of embl. > > Cheers, > Steffen > >> Thanks, for the recommendation. >> >> So far, I just read Steffen's and your biomaRt user?s guide and had a >> look at the BioMart 0.7 Documentation, since I needed quick results. >> I'm going to have a look at the recommended book and paper, now. >> >> >> In the meantime, I got to a solution - but not a very satisfying one: >> >> ensembl = useDataset("hsapiens_gene_ensembl", mart=ensembl) >> >> myAttributes = c("embl", "cdna", "5utr", "coding", "3utr", "5_utr_end", >> "3_utr_start", "sequence_cdna_length","cds_length") >> >> ... >> >> qresult = getBM(attributes=myAttributes, >> filters=..., >> values=..., >> mart=ensembl) >> >> finalResult = mySeqCdsLengthFilter(qresult, c(3000, 5000), c(2000, 3000)) >> >> For now, I parse my query results manually, using >> the values for "sequence_cdna_length" and "cds_length" as limits. >> I wish these attributes were filters ... >> or there was a BioMart and a database, I could use in a linked query via >> getLDS. >> >> I'm still curious for a smarter solution. >> >> >> Best regards, >> Simon >> >> >> Wolfgang Huber wrote: >>> Hi Simon, >>> >>> with all respect, for a first contact with the Bioconductor project I'd >>> also recommend studying some of the documentation. >>> >>> A (slightly biased) set of points to start with are the "Bioconductor >>> Case Studies" book by Hahne, Huber, Gentleman, Falcon and the paper >>> "Mapping identifiers for the integration of genomic datasets with the >>> R/Bioconductor package biomaRt." by Durinck et al. in Nature Protocols >>> 2009;4(8):1184-91. >>> >>> Best wishes >>> Wolfgang >>> >>> >>> >>> >>> Simon ha scritto: >>>> Hello everybody, >>>> >>>> I am trying to solve the following tasks as a first contact with the >>>> bioconductor project: >>>> >>>> # Task 1: >>>> # find: >>>> # * mRNA sequence (5'UTR, Coding region, 3'UTR) >>>> # * position of start codon in sequence >>>> # * position of stop codon in sequence >>>> # * ID (Which ID(s) would I choose to reference my >>>> # sequence hits? Embl, ensembl transcript id, >>>> # Entrez Gene id, RefSeq, etc.?) >>>> # * name of associated protein product >>>> # >>>> # where: >>>> # * origin is human >>>> # Entrez Search would be: human[ORGN] >>>> # * sequence is mRNA transcript >>>> # Entrez Search for Molecule Type: biomol_mRNA[PROP]? >>>> # * mRNA sequence length is 3000 to 5000 nts >>>> # * Entrez Search for Sequence Length: 3000:5000[SLEN] >>>> # * coding region of mRNA length is 2000 to 3000 nts >>>> # * Entrez Search Field for stop and start of >>>> # coding region: start:stop[CDS] >>>> # >>>> # >>>> # Task 2: >>>> # store the retrieved information to file for the first 200 hits >>>> # (Which would be a suitable file formate?) >>>> >>>> I started by using and playing around with the biomaRt package for R, >>>> but I got overwhelmed by its many possibilities. >>>> >>>> I would be glad to get any feedback, on how to start or even solve my >>>> tasks. >>>> >>>> Best regards, >>>> Simon >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >