Hello Everyone
I have a fasta file of seed sequences. It looks like this
>hsa-miR-140-5p_1_8
AACCACTG
>hsa-miR-140-5p_1_7
ACCACTG
>hsa-miR-140-5p_1_6
CCACTG
>hsa-miR-140-5p_2_8
AACCACT
>hsa-miR-140-5p_2_7
ACCACT
This fasta file consists of miRNA seed sequences and the maximum seq length is 8 and minimum is 6. lets name it as seed.fa
Also I have created a fasta file of miRNA sequences lets say miRNA.fa
I would like to search this miRNA.fa file for seed sequences in file seed.fa
I built the index of the miRNA.fa using bowtie-build and then used this command for alignment
/apps1/bowtie -n 0 -a --sam --threads 2 /BOWTIE/index -f seed.fa > seed_out.fa.sam
I purposely used n as 0 because i don't want any mismatches in the seed itself(as they are very small).
Is there any other way i can do the seed search for file seed.fa for my miRNA.fa sequences
Let me know
Thanks
Varun
Why don;t you try SHRiMP2 aligner in miRNA alignment mode. They have also explained what seeds to use when aligning miRNAs. http://compbio.cs.toronto.edu/shrimp/README Ctrl+F "miRNA"