[BioC] how to get pig genome and for miRNA target scan

[José Afonso Guerra-Assunção]

Not all transcripts have defined UTRs, this is normal.
Regards,
A.

On Thu, Mar 15, 2012 at 12:59, wang peter <wng.peter at gmail.com> wrote:
> dear sean：
>
> The 3' UTR data can be retrieved
> but some are missing, i donot know why
>
> dataset1 <-useDataset(dataset="sscrofa_gene_ensembl",mart=mart)
> attributes <- listAttributes(dataset1)
> seq = getSequence(chromosome=1,start=1, end=50000,
> type="ensembl_gene_id", seqType="3utr", mart = dataset1)
>
>
>
> "3utr"  "ensembl_gene_id"
> "1"     "Sequence unavailable"  "ENSSSCG00000004013"
> "2"     "Sequence unavailable"  "ENSSSCG00000004017"
> "3"     "CTTGTTCCACGTACCAAAGAGTGCTTGCTTCTCACCTTTTCAGAAACACACGCCATTATATTATAGAGTTGGAAACATCACA"    "ENSSSCG00000004009"
> "4"     "CCTGAGCCGGGGACTGTGACAGGCTCCTCCTCCTGCCCGTGGCTGGCTGTACCTACGCCCCCTCCTGCTGGTGGCCTTCCTGCTCCCTTCAAGGGTCCCCCTTATTGCGAAAGGAGAAATGAATGGCATCCGGGACTTCTGCACAGAATTTGGTAAAGTTAAAATAAAGAAAAAAAAACAA" "ENSSSCG00000004008"
> "5"     "GGT"   "ENSSSCG00000004019"
> "6"     "Sequence unavailable"  "ENSSSCG00000004014"
> "7"     "Sequence unavailable"  "ENSSSCG00000004018"
> "8"     "Sequence unavailable"  "ENSSSCG00000004012"
> "9"     "Sequence unavailable"  "ENSSSCG00000004015"
> "10"    "Sequence unavailable"  "ENSSSCG00000004007"
> --
> shan gao
> Room 231(Dr.Fei lab)
> Boyce Thompson Institute
> Cornell University
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