likelihood of number of consecutive Ns in miRNA sequence

Question

[realnewbie]

Hi, Dear community,

I have a very interesting question. I am planning to count the number of sequences with greater than some consecutive number of nucletodies (i.e number of sequences with >=5 Gs) as empty product. Do you have any idea about the likelihood of consecutive Ns in miRNA sequences?

ps: I am not asking 25% expected ratio of each base. I am asking the likelihood of presence of GGGGG like patterns in short miRNA sequences?

Many thanks, Best regards,

[GenoMax]

Why should there be any N's in sequence for a run that has worked well?

[Jeremy Leipzig]

I think the OP means any mononucleotide kmer?

[GenoMax]

Ah yes. That must be it.

Answer 1

[Jeremy Leipzig]

this should be as simple as downloading the hairpins or mature sequences and looking for your patterns

perl -ne '$x=5;if(/>/){if ($seq){$seq =~ m/((A{$x,}|C{$x,}|G{$x,}|U{$x,}))/ && print $def.$1."\n";}$seq="";$def=$_;}else{chomp;$seq=$seq.$_;}' hairpin.fa 
>cel-mir-38 MI0000009 Caenorhabditis elegans miR-38 stem-loop
UUUUUU
>cel-mir-41 MI0000012 Caenorhabditis elegans miR-41 stem-loop
UUUUU
>cel-mir-42 MI0000013 Caenorhabditis elegans miR-42 stem-loop
UUUUU
>cel-mir-49 MI0000020 Caenorhabditis elegans miR-49 stem-loop
AAAAA
>cel-mir-51 MI0000022 Caenorhabditis elegans miR-51 stem-loop
AAAAA