Alignment viewer?
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Erik Wright ▴ 210
@erik-wright-4003
Last seen 10.3 years ago
Hi all, Does anyone know of a package that I can use to view alignments in R? Basically I want to display a long DNAStringSet sequence by sequence: Seq1: ACTAGGAGCTYA... Seq2: ACTACGAGCTCA... Seq3: ACTAGGACCTNA... etc.... I just wanted to check if there is one already available so that I don't go off and reinvent the wheel. Thanks!, Erik
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Thomas Girke ★ 1.7k
@thomas-girke-993
Last seen 9 months ago
United States
If it helps, here are a few examples for handling multiple/pairwise alignments in Biostring's XStringSet container class and viewing them as html files in a browser (StringSet2html): http://manuals.bioinformatics.ucr.edu/home/ht-seq#TOC-Multiple- Sequence-Alignments-MSAs- It wouldn't be difficult to add color coding to this html-based viewing option. One question I would ask the developers of Biostrings is whether they are planning to release a specific object class for handling multiple alignments in the future. For me XStringSet works just great for analyzing and manipulating multiple alignments.. Thomas On Tue, May 04, 2010 at 03:33:19PM -0700, Erik Wright wrote: > Hi all, > > Does anyone know of a package that I can use to view alignments in R? Basically I want to display a long DNAStringSet sequence by sequence: > Seq1: ACTAGGAGCTYA... > Seq2: ACTACGAGCTCA... > Seq3: ACTAGGACCTNA... > etc.... > > I just wanted to check if there is one already available so that I don't go off and reinvent the wheel. > > Thanks!, > Erik > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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Very good idea! Thanks Thomas! On May 4, 2010, at 4:30 PM, Thomas Girke wrote: > If it helps, here are a few examples for handling multiple/pairwise > alignments in Biostring's XStringSet container class and viewing them as > html files in a browser (StringSet2html): > http://manuals.bioinformatics.ucr.edu/home/ht-seq#TOC-Multiple- Sequence-Alignments-MSAs- > > It wouldn't be difficult to add color coding to this html-based viewing option. > > One question I would ask the developers of Biostrings is whether they > are planning to release a specific object class for handling multiple > alignments in the future. For me XStringSet works just great for > analyzing and manipulating multiple alignments.. > > Thomas > > > On Tue, May 04, 2010 at 03:33:19PM -0700, Erik Wright wrote: >> Hi all, >> >> Does anyone know of a package that I can use to view alignments in R? Basically I want to display a long DNAStringSet sequence by sequence: >> Seq1: ACTAGGAGCTYA... >> Seq2: ACTACGAGCTCA... >> Seq3: ACTAGGACCTNA... >> etc.... >> >> I just wanted to check if there is one already available so that I don't go off and reinvent the wheel. >> >> Thanks!, >> Erik >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>
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On Tue, May 4, 2010 at 4:30 PM, Thomas Girke <thomas.girke@ucr.edu> wrote: > If it helps, here are a few examples for handling multiple/pairwise > alignments in Biostring's XStringSet container class and viewing them as > html files in a browser (StringSet2html): > > http://manuals.bioinformatics.ucr.edu/home/ht-seq#TOC-Multiple- Sequence-Alignments-MSAs- > > It wouldn't be difficult to add color coding to this html-based viewing > option. > > One question I would ask the developers of Biostrings is whether they > are planning to release a specific object class for handling multiple > alignments in the future. This has been on the table for a while, I think. We need to initiate a more serious discussion during this release cycle. Michael > For me XStringSet works just great for > analyzing and manipulating multiple alignments.. > > Thomas > > > On Tue, May 04, 2010 at 03:33:19PM -0700, Erik Wright wrote: > > Hi all, > > > > Does anyone know of a package that I can use to view alignments in R? > Basically I want to display a long DNAStringSet sequence by sequence: > > Seq1: ACTAGGAGCTYA... > > Seq2: ACTACGAGCTCA... > > Seq3: ACTAGGACCTNA... > > etc.... > > > > I just wanted to check if there is one already available so that I don't > go off and reinvent the wheel. > > > > Thanks!, > > Erik > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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A colleague sent me the following snippet. I'm not really familiar with the package, but it sounds like he needs to load a library, or use a different input file. Suggestion from this wise group would be appreciated. Best, Tom --- You wrote: x.lumi<-lumiR(fileName,lib="lumiHumanIDMappng") --- end of quote --- I got a warning message: In addNuID2lumi(x.lumi, lib.mapping = lib.mapping) : lumiHumanIDMappng does not include nuID conversion information!
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first, follow the posting guide. provide sessionInfo() result. second, note the spelling error. "mappng" is not "mapping" On Wed, May 5, 2010 at 10:45 AM, Thomas Hampton < thomas.h.hampton@dartmouth.edu> wrote: > A colleague sent me the following snippet. I'm not really familiar with > the package, but it sounds like he needs to load a library, or use a > different input file. Suggestion from this wise group would be appreciated. > > Best, > > Tom > > > --- You wrote: > x.lumi<-lumiR(fileName,lib="lumiHumanIDMappng") > --- end of quote --- > > I got a warning message: > > In addNuID2lumi(x.lumi, lib.mapping = lib.mapping) : > lumiHumanIDMappng does not include nuID conversion information! > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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Hi Tom, The nature of your question is not very clear to me, but the details of nuIDs and which kinds of packages etc. are needed is is all explained in the vignettes for the lumi package. You can see them here: http://www.bioconductor.org/packages/release/bioc/html/lumi.html If you still have questions, please let us know. Marc On 05/05/2010 07:45 AM, Thomas Hampton wrote: > A colleague sent me the following snippet. I'm not really familiar with > the package, but it sounds like he needs to load a library, or use a > different input file. Suggestion from this wise group would be > appreciated. > > Best, > > Tom > > > --- You wrote: > x.lumi<-lumiR(fileName,lib="lumiHumanIDMappng") > --- end of quote --- > > I got a warning message: > > In addNuID2lumi(x.lumi, lib.mapping = lib.mapping) : > lumiHumanIDMappng does not include nuID conversion information! > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
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Hi, Tom It looks the lumiHumanAll.db is not loaded. Please provide more detailed information, for example, sessionInfo(), species, etc. Thanks Gilbert On 5/5/10 9:45 AM, "Thomas Hampton" <thomas.h.hampton at="" dartmouth.edu=""> wrote: > A colleague sent me the following snippet. I'm not really familiar with > the package, but it sounds like he needs to load a library, or use a > different input file. Suggestion from this wise group would be > appreciated. > > Best, > > Tom > > > --- You wrote: > x.lumi<-lumiR(fileName,lib="lumiHumanIDMappng") > --- end of quote --- > > I got a warning message: > > In addNuID2lumi(x.lumi, lib.mapping = lib.mapping) : > lumiHumanIDMappng does not include nuID conversion information! > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
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And in addition Biostrings has the functions consensusString and consensusMatrix which, in combinantion with package seqLogo, can be used to create a sequence logo from your multiple alignment in R. Regards, Joern On Tue, 4 May 2010 16:30:04 -0700, Thomas Girke wrote > If it helps, here are a few examples for handling multiple/pairwise > alignments in Biostring's XStringSet container class and viewing > them as html files in a browser (StringSet2html): > http://manuals.bioinformatics.ucr.edu/home/ht-seq#TOC-Multiple- > Sequence-Alignments-MSAs- > > It wouldn't be difficult to add color coding to this html-based > viewing option. > > One question I would ask the developers of Biostrings is whether they > are planning to release a specific object class for handling multiple > alignments in the future. For me XStringSet works just great for > analyzing and manipulating multiple alignments.. > > Thomas > > On Tue, May 04, 2010 at 03:33:19PM -0700, Erik Wright wrote: > > Hi all, > > > > Does anyone know of a package that I can use to view alignments in R? Basically I want to display a long DNAStringSet sequence by sequence: > > Seq1: ACTAGGAGCTYA... > > Seq2: ACTACGAGCTCA... > > Seq3: ACTAGGACCTNA... > > etc.... > > > > I just wanted to check if there is one already available so that I don't go off and reinvent the wheel. > > > > Thanks!, > > Erik
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