hi james,
thanks, I know .... my question is how to get a genomic dna sequence (where
there maybe is no gene) ???
any ideas ?
kind regards
mayra

On Thu, Aug 13, 2009 at 2:53 PM, James W. MacDonald
<jmacdon@med.umich.edu>wrote:

> Hi Mayra,
>
>
> Mayra Eduardoff wrote:
>
>> Hi Steffen
>>
>>
>> I want to retrieve a genomic sequence with biomaRt:
>>
>>
>> Session(info)
>> R version 2.9.1 (2009-06-26)
>> i386-pc-mingw32
>>
>> locale:
>>
>> LC_COLLATE=German_Austria.1252;LC_CTYPE=German_Austria.1252;LC_MONETARY=German_Austria.1252;LC_NUMERIC=C;LC_TIME=German_Austria.1252
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>>  [1] BSgenome_1.12.3         cureos_0.3              Biostrings_2.12.8
>> IRanges_1.2.3           zfv2.db_1.0.0           RSQLite_0.7-1
>>  [7] DBI_0.2-4               Agi4x44PreProcess_1.4.0 genefilter_1.24.2
>> annotate_1.22.0         AnnotationDbi_1.6.1     venn_1.5
>> [13] multtest_2.1.1          vsn_3.12.0              Biobase_2.5.5
>> xtable_1.5-5            limma_2.18.2            biomaRt_2.0.0
>>
>>
>>
>>  mart <- useMart("ensembl")
>>> mart <- useDataset(mart=mart, "drerio_gene_ensembl")
>>>
>>
>> seq <- getSequence(chromosome = 15, start = 18357968, end = 18360987, mart
>> =
>> mart)
>>
>> Fehler in getSequence(chromosome = 15, start = 18357968, end = 18360987,
>>  :
>>  Please specify the type of sequence that needs to be retrieved when using
>> biomaRt in web service mode.  Choose either gene_exon,
>> transcript_exon,transcript_exon_intron, gene_exon_intron, cdna,
>>
>> coding,coding_transcript_flank,coding_gene_flank,transcript_flank,gene_flank,peptide,
>> 3utr or 5utr
>>
>> Apart from the fact that I want a genomic region even if I specify type it
>> doesn t seem to work :
>>
>> seq <- getSequence(chromosome = 15, start = 18357968, end = 18360987,
>> type="gene_exon", mart = mart)
>> Fehler in getSequence(chromosome = 15, start = 18357968, end = 18360987,
>>  :
>>  Please specify the type of sequence that needs to be retrieved when using
>> biomaRt in web service mode.  Choose either gene_exon,
>> transcript_exon,transcript_exon_intron, gene_exon_intron, cdna,
>>
>> coding,coding_transcript_flank,coding_gene_flank,transcript_flank,gene_flank,peptide,
>> 3utr or 5utr
>>
>>
>> or  as in documentation (although this doesn t make any sense to me to
>> specify seqType and type...)
>>
>
> You have to specify seqType and type because the sequences don't come back
> in the same order you requested, so the type argument is used to label the
> sequences.
>
> Also, I don't see any way to get inter-genic sequences. For instance:
>
> > getSequence(15,18357968,18360987,seqType="cdna", mart=mart,
> type="ensembl_transcript_id")
> [1] cdna                  ensembl_transcript_id
> <0 rows> (or 0-length row.names)
>
> Because this portion of the zebrafish genome contains no known genes.
> However, if I pick a region that does contain a gene:
>
> > getSequence(15,18723006,18741517,seqType="cdna", mart=mart,
> type="ensembl_transcript_id")
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>                                                                    cdna
> 1
> AGGAGCCGCTCAGACCACACCAGTGCAGGGTCAGAACCTGGTGACAAATAATGTCTCAGTGGTGGAGGGCGAGACGGCCATCATCAGCTGCCGGGTGAAAAACAACGACGACTCCGTCATCCAACTGCTCAACCCCAACCGGCAGACTATCTACTTCAGAGACGTTAGACCTTTGAAGGACAGTCGGTTTCAGCTGGTAAACTTCTCCGACAACGAGCTCTTGGTGTCCCTGTCCAACGTGTCTCTGTCGGACGAGGGCCGCTACGTGTGTCAACTCTACACGGATCCACCGCAAGAAGCCTACGCCGACATCACTGTACTGGTTCCACCAGGCAACCCAATCTTAGAGTCCCGCGAGGAAATCGTGAGCGAGGGGAATGAGACCGAGATAACCTGCACCGCCATGGGCAGCAAACCTGCTTCCACCATCAAATGGATGAAAGGCGACCAACCACTGCAAGGTGAGGCGACTGTGGAGGAGTTATACGACAGGATGTTCACTGTCACCAGCCGGCTCAGGCTCACCGTCTCTAAGGAGGACGATGGAGTGGCCGTCATCTGCATCATTGACCATCCAGCCGTGAAGGACTTCCAGGCCCAGAAATACCTGGAAGTGCAGTATAAACCAGAAGTGAAGATTGTGGTGGGATTCCCAGAGGGTTTGACCAGAGAAGGAGAAAATCTCGAGCTGACATGCAAAGCTAAAGGAAAACCGCAGCCTCATCAAATTAACTGGCTCAAAGTGGATGATGATTTCCCCTCCCACGCCTTGGTAACTGGCTCTGATCTCTTCATCGAAAACCTTAACAAGTCCTACAACGGAACGTACCGCTGTGTGGCATCTAACTTAGTGGGAGAAGCCTACGATGATTACATCCTTTATGTATACGATTCAAGAGCAGATGGAGCGCCACAGAAAATTGATCATGCCGTCATCGGCGGAGTTGTCGCAGTGGTTGTGTTCGCCATGCTTTGTCTCCTGATTGTTC
>
> TTGGCCGATATTTCGCCAGACACAAAGGGACCTACTTCACCCACGAAGCTAAAGGAGCGGATGACGCGGCGGACGCCGACACTGCCATCATCAACGCAGAGGGCGGACACAACAATTCGGATGACAAGAAGGAATACTACATTTAA
>  ensembl_transcript_id
> 1    ENSDART00000062603
>
> Best,
>
> Jim
>
>
>
>
>> seq <- getSequence(chromosome = 15, start = 18357968, end = 18360987,
>> type="entrez", seqType="cdna", mart = mart)
>> Fehler in getBM(c(seqType, type), filters = c("chromosome_name", "start",
>>  :
>>
>> Invalid attribute(s): entrez
>> Please use the function 'listAttributes' to get valid attribute names
>>
>>
>>
>>
>> I  can t load  in msyql mode either anymore :
>>  mart <- useMart("ensembl", mysql=TRUE)
>> Fehler: mysql access to Ensembl is no longer available through this
>> package
>> the web service mode supports all queries.  If mysql is needed a separate
>> package will become available with limited mysql query support.
>>
>>
>> I would be very greatful for you help !
>>
>>
>> kind regards,
>>
>> Mayra
>>
>>
> --
> James W. MacDonald, M.S.
> Biostatistician
> Douglas Lab
> University of Michigan
> Department of Human Genetics
> 5912 Buhl
> 1241 E. Catherine St.
> Ann Arbor MI 48109-5618
> 734-615-7826
>



-- 
Mayra Eduardoff
Institute of Molecular Biology
University of Innsbruck
Viktor-Franz Hess Haus
Technikerstrasse 25
6020 Innsbruck
Tel: +43 512 507 6286
email: mayra.eduardoff@student.uibk.ac.at

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