---------- Forwarded message ---------- From: wang peter <wng.peter@gmail.com> Date: Mon, Nov 7, 2011 at 1:25 PM Subject: the procedure to annotate assembled transcriptom To: bioc-sig-sequencing@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 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 [[alternative HTML version deleted]]

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 > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >