Convert Fasta format to MEME-motif format
2
4
Entering edit mode
3.3 years ago
kashiff007 ★ 1.8k

Repeat sequences, such as 45S rDNA (gene) and many tandem repeats distributed throughout the genome. These repeats can identical in its sequence or they may vary at few nucleotide positions.

I know they can be scan through FIMO (which is program from MEME-Suite) for their location in whole genome. But FIMO required MEME-motif file which mainly contain "letter-probability matrix". MEME motif file example is shown below:

MEME version 4

ALPHABET= ACGT

strands: +

Background letter frequencies

A 0.25 C 0.25 G 0.25 T 0.25


MOTIF MA0002.1 RUNX1

letter-probability matrix: alength= 4 w= 18 nsites= 18 E= 1.1e-006
0.611111 0.000000 0.055556 0.333333
0.555556 0.000000 0.111111 0.333333
0.222222 0.166667 0.222222 0.388889
0.000000 0.111111 0.000000 0.888889
0.000000 0.055556 0.944444 0.000000
0.111111 0.000000 0.000000 0.888889
0.055556 0.000000 0.888889 0.055556
0.833333 0.111111 0.055556 0.000000
0.111111 0.388889 0.277778 0.222222
0.333333 0.055556 0.500000 0.111111
0.111111 0.222222 0.111111 0.555556
0.277778 0.222222 0.222222 0.277778
0.111111 0.055556 0.722222 0.111111
0.388889 0.166667 0.055556 0.388889
0.055556 0.000000 0.111111 0.833333
0.055556 0.777778 0.000000 0.166667
0.777778 0.000000 0.222222 0.000000
0.277778 0.611111 0.055556 0.055556

I have read the MEME motif format (http://meme-suite.org/doc/meme-format.html) in detail. I have problem in understanding the concept behind generating the "letter-probability matrix" in MEME-motif format. They also have not mentioned any software/script which directly converts fasta format to MEME-motif.

So, I have two questions regarding this:

  • How to convert single fasta file into this MEME-motif file?
  • In case I have multiple copy of fasta file of such tandem repeats which are varying at few location only, how to convert these fasta files into one MEME-motif file?
MEME-suite FIMO motif fasta format conversion • 2.3k views
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4
Entering edit mode
3.3 years ago
kashiff007 ★ 1.8k

Follow these steps:

  • Generate background files by: fasta-get-markov
  • Use iupac2meme to generate MEME motif file
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3
Entering edit mode
3.3 years ago
kashiff007 ★ 1.8k

Full FIMO Pipeline Step

fasta-get-markov sequences.fasta > sequences.bg
mkdir temp
fasta-grep '.+' -dna -o < motif_sites.fasta > temp/motif_name.txt
sites2meme -bg sequences.bg temp > motif_name.meme
fimo --bgfile  sequences.bg motif_name.meme Genome_to_be_search.fasta
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