User: oliwindram

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oliwindram10
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United Kingdom
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3 years, 3 months ago
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4 years, 2 months ago
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Posts by oliwindram

<prev • 6 results • page 1 of 1 • next >
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Mapping sequence features to alignments
...   Hi I am trying to work out how to relate basepair position information in unaligned sequence to aligned sequences in pairwiseAlignment objects. So if I have a feature in my initial unaligned pattern or subject sequence at 100-110 bp I would like to be able to identify where this in the aligned se ...
pairwisealignment indel written 3.3 years ago by oliwindram10 • updated 3.3 years ago by Hervé Pagès ♦♦ 14k
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Answer: A: getBackgroundFrequencies for Arabidopsis
... That is great thanks ...
written 4.2 years ago by oliwindram10
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getBackgroundFrequencies for Arabidopsis
...   Hi I am trying to use PWMEnrich to look for promoter enrichment in a group of Arabidopsis genes. As the Arabidopsis genome is not supported I am trying to create the relevant backgrounds etc I tried the command bellow and got the following: > genomic.acgt = getBackgroundFrequencies(BSgenom ...
bsgenome pwmenrich written 4.2 years ago by oliwindram10
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Comment: C: Working with Arabidopsis Databases
... This seems to have solved the problem: seqlevels(TxDb.Athaliana.BioMart.plantsmart25) <- seqlevels(BSgenome.Athaliana.TAIR.TAIR9) chrommyb108.loc <- transcriptsBy(TxDb.Athaliana.BioMart.plantsmart25, by="gene") [myb108] isCircular(chrommyb108.loc) <- isCircular(BSgenome.Athaliana.TAIR.TAI ...
written 4.2 years ago by oliwindram10
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Answer: A: Working with Arabidopsis Databases
...   Hi Hervé, Thanks for your comment,  this does help to a degree it changes the seqnames. However the isCircular statement for ChrC which I imagine is the plastid chromosome still differs between the two? I think this is what is causing the error I am getting now which is: > promoter.myb108 &l ...
written 4.2 years ago by oliwindram10
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Working with Arabidopsis Databases
... Hi  I have been trying to follow this tut (http://www.bioconductor.org/help/workflows/gene-regulation-tfbs/#sequence-search) and apply it to working with some gene in Arabidopsis. I try this: library(MotifDb) library(seqLogo) library(motifStack) library(Biostrings) library(GenomicFeatures) librar ...
bsgenome biomart getpromoterseq txdb written 4.2 years ago by oliwindram10

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Popular Question 3.3 years ago, created a question with more than 1,000 views. For Working with Arabidopsis Databases

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