Entering edit mode
9.9 years ago
shaanbdu
•
0
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:
- Extract the alignment sequence from the EST.
- Attach 100 left and right flanking sequences to this 'hit'.
- 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.
- Print all the possible hits+flanking sequences as new fasta files.