Find Motifs in Genome

Question

[fire_water]

I am wondering if a tool already exists to accomplish the following task...

First, the motifs of interest:

• CATGTG
• CATTTG
• CACGTG

Second, the pattern to find in the genome:

any motif 6-7nt any motif

Finally, the expected output:

chr, start (of motif), gap (# nt between: 6 or 7)

For example:

• chromosome: chr1
• sequence: ATTCATGTGxxxxxxCATTTGCCG
• output: chr1, 4, 6

I can write it myself but I would prefer not to reinvent the wheel. Thanks!

[Medhat]

can you see if one of these tools will do what you need?

fuzznuc
FIMO
HIMER

Answer 1

[shenwei356]

My wheel, seqkit (please update to the v0.4.4+ version)

seqkit locate (usage) is used to locate subsequences/motifs. Motifs could be EITHER plain sequence containing ACTGN OR regular expression (default) like A[TU]G(?:.{3})+?[TU](?:AG|AA|GA) for ORFs. Degenerate bases like RYMM.. are also supported by flag -d.

$ cat motifs.fa 
>CATGTG
CATGTG
>CATTTG
CATTTG
>CACGTG
CACGTG
>motif4
CATTTG.{6,7}CACGTG

$ cat seqs.fa 
>seq1
tactgCATGTGactangcgang
>seq2
cccCATTTGttttttCACGTGttt
>seq3
cccCATTTGttttCACGTGttt

$ seqkit locate -i -f motifs.fa seqs.fa | column -t
seqID  patternName  pattern             strand  start  end  matched
seq1   CATGTG       CATGTG              +       6      11   CATGTG
seq2   CATTTG       CATTTG              +       4      9    CATTTG
seq2   CACGTG       CACGTG              +       16     21   CACGTG
seq2   CACGTG       CACGTG              -       16     21   CACGTG
seq2   motif4       CATTTG.{6,7}CACGTG  +       4      21   CATTTGttttttCACGTG
seq3   CATTTG       CATTTG              +       4      9    CATTTG
seq3   CACGTG       CACGTG              +       14     19   CACGTG
seq3   CACGTG       CACGTG              -       14     19   CACGTG

Sorry, you must count the gaps by yourself.