[BioC] the procedure to annotate assembled transcriptom

[Sean Davis]

On Mon, Nov 7, 2011 at 1:26 PM, wang peter <wng.peter at gmail.com> wrote:
> ---------- Forwarded message ----------
> From: wang peter <wng.peter at gmail.com>
> Date: Mon, Nov 7, 2011 at 1:25 PM
> Subject: the procedure to annotate assembled transcriptom
> To: bioc-sig-sequencing at r-project.org
>
>
> dear all:
>        i have some assembled transcriptom without referenced genomes.
> i need annotate them based on NCBI nr or swissprot databases.
>
> one choice is use blast, and then write some perl scripts to extract the
> annotation

You might try using blast with the -m 8 format, which is
tab-delimited-text.  That output can be easily parsed by R.  There are
many options for doing this type of thing, though.

Sean


> the other one is R package.
>
> so which one is better? i donot know if R can deal with so big databse,like
> NCBI nr or swissprot databases.
> who have R pipeline or script coding to share with me?
> thank you very much
>
> gao shan
>
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