Covert multiple short sequence into list of IUPAC motif
Hi, I have approximately 200 four nucleotide base sequences, I want to cluster them into various repeat/motif and get final IUPAC notation of them.
For example :
AAAC
AAAG
CCAA
CTCA
CTCC
TGGT
TTAG
TTCA
Let me know if anyone have some suggestion.
Thanks you in advance.
1 answer
Look into the R package DiffLogo. You can convert your fasta file into a PWM which you can then use elsewhere. Looks like universalmotif might also have a bunch of packages relevant to you http://www.bioconductor.org/packages/devel/bioc/vignettes/universalmotif/inst/doc/MotifManipulation.pdf
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please, review all your previous questions and mark they answered if needed (green tick on the left). eg: Extracting Intron-Exon Reads from bam files , how to extract intron coordinates (in bed) from bam , etc...
You could do a multiple sequence alignment and then create a sequence logo from it. There is a web based version: https://weblogo.berkeley.edu/logo.cgi