I am working on miRNA identification in plants and for this I initially ran a blast with EST sequences as queries against the mine database. Now when I have got the output file, I want to extract the regions aligned with the existing miRNAs with 100 flanking sequences from both ends as separate fasta files, which I would use for running a blastx later. Also, some of the alignments are made with the minus strand and therefore, such sequences need to be converted into a reverse complementary form first. Can anyone help me with a program that can:
1. Extract the alignment sequence from the EST.
2. Attach 100 left and right flanking sequences to this 'hit'.
3. Check if the alignment is with the plus or minus strand, and if the alignment is with the minus strand, convert the output sequence to a reverse complementary sequence.
4. Print all the possible hits+flanking sequences as new fasta files.