Hi All, I have use the BLAST program provided by NCBI to compare large databases and have generated a lot of output in one long text file. I was looking for a way to parse out the results in a nice way so that it could be easily visualized. I was thinking of trying to write something in R, but I wanted to check in with the help group to make sure I am not re-inventing the wheel. Any help would be great! Matt Oliver
On Fri, 19 Mar 2004 11:46:25 -0500 (EST), Matthew Oliver <oliver at imcs.marine.rutgers.edu> wrote :>Hi All, > >I have use the BLAST program provided by NCBI to compare large databases and have >generated a lot of output in one long text file. I was looking for a way to parse >out the results in a nice way so that it could be easily visualized. I was thinking >of trying to write something in R, but I wanted to check in with the help group to >make sure I am not re-inventing the wheel. Any help would be great!I don't know if this is there or not, but the Bioconductor project (bioconductor.org) is a likely place to look for something like that. Duncan
Matt - Yes, you would be seriously re-inventing the wheel. A standard tool is the bioperl SearchIO package. This is described at www.bioperl.org > Docs > SearchIO HOWTO: The html version of that link evaluates to: http://bioperl.org/HOWTOs/html/SearchIO.html - best - tom blackwell - u michigan medical school - ann arbor - On Fri, 19 Mar 2004, Matthew Oliver wrote:> Hi All, > > I have use the BLAST program provided by NCBI to compare large databases and have > generated a lot of output in one long text file. I was looking for a way to parse > out the results in a nice way so that it could be easily visualized. I was thinking > of trying to write something in R, but I wanted to check in with the help group to > make sure I am not re-inventing the wheel. Any help would be great! > > Matt Oliver > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://www.stat.math.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html >