Covert multiple short sequence into list of IUPAC motif

Question

[praasu]

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.

[Pierre Lindenbaum]

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...

[GenoMax]

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

Answer 1

[Trivas]

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