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Question: BLAST in R
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gravatar for Zoha Moztarzadeh
7.5 years ago by
Zoha Moztarzadeh20 wrote:
Hello bioconductor group, I have a FASTA sequences (without ID) and would like to find the homolge sequneces with BLAST. How can I do this in R explain me haw to do multiple sequence alignment with them. Thanks in advance, Zoha [[alternative HTML version deleted]]
ADD COMMENTlink modified 3.0 years ago by mhahsler20 • written 7.5 years ago by Zoha Moztarzadeh20
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gravatar for mhahsler
3.0 years ago by
mhahsler20
United States
mhahsler20 wrote:

Using BLAST from R is now easy with rBLAST (see https://github.com/mhahsler/rBLAST).

ADD COMMENTlink written 3.0 years ago by mhahsler20
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gravatar for Hervé Pagès
7.5 years ago by
Hervé Pagès ♦♦ 13k
United States
Hervé Pagès ♦♦ 13k wrote:
Hi Zoha, On 11-06-06 07:49 AM, Zoha Moztarzadeh wrote: > Hello bioconductor group, > > I have a FASTA sequences (without ID) and would like to find the homolge sequneces with BLAST. > How can I do this in R explain me haw to do multiple sequence alignment with them. The only thing I'm aware of is the blastSequences() function in the annotate package. I've never used this function. Cheers, H. > > Thanks in advance, > > Zoha > [[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 -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319
ADD COMMENTlink written 7.5 years ago by Hervé Pagès ♦♦ 13k
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gravatar for January Weiner
7.5 years ago by
January Weiner370 wrote:
Dear Zoha, I think the simplest thing to do is to invoke the command line blast from R, using the option -m 8 to get tabular output that can be automatically parsed by read.table. Example: myPipe <- pipe( "blastall -p blastp -i text.fasta -d data.fasta" ) results <- read.table( myPipe ) colnames( blastResults ) <- c( "QueryID", "SubjectID", "Perc.Ident", "Alignment.Length", "Mismatches", "Gap.Openings", "Q.start", "Q.end", "S.start", "S.end", "E", "Bits" ) However, that way you will not get the actual alignments. Cheers, j. On Mon, Jun 6, 2011 at 4:49 PM, Zoha Moztarzadeh <zoha_mozt at="" yahoo.com=""> wrote: > Hello bioconductor group, > > I have a FASTA sequences (without ID) and would like to find the homolge sequneces with BLAST. > How can I do this in R explain me haw to do multiple sequence alignment with them. > > Thanks in advance, > > Zoha > ? ? ? ?[[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 > -- -------- Dr. January Weiner 3 -------------------------------------- Max Planck Institute for Infection Biology Charit?platz 1 D-10117 Berlin, Germany Web?? : www.mpiib-berlin.mpg.de Tel? ?? : +49-30-28460514
ADD COMMENTlink written 7.5 years ago by January Weiner370
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