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plant miRNA target alignment>>
You can also download Command-line version, Window version, and Source code
FIY: If you have more than 20 microRNAs and a larger target database, we strongly recommend you to download the Command-line version or the Window version and run Target-align on your machine, due to the completion of a running would be a little long. Thank you!
Target-align can be run on Linux!!! 2/14/2012
Target-Align can be run on Linux if you set up Mono on your linux system. All file names are interpreted in upper case based on Mono. Suppose I have a miRNA file named in seq1 and a target file named seq2. The following command works:
./TargetAlign.exe -m SEQ1 -d SEQ2 -o RESULTFILE -sc 45 -maxmismatches 4 -secMaxMismatches 2 -secMaxStart 1 -secMaxEnd 9 -noMismatchesStart 10 -noMismatchesEnd 11 -allowGU T -maxGU 6 -GUmismatch 0.5 -maxGap 4 -matchScore 5 -GUScore 2 -xnScore -1 -otherMatchScore -3 -gapOpenScore -8 -gapExtendScore -2
So, if you want to use Target-Align on Linux, please name all your files in upper case!
Cheers!

If you use Target-align in your research, please cite us:

Xie F, Zhang B. 2010. Target-align: a tool for plant microRNA target identification. Bioinformatics. 26 (23): 3002-3.

Sequence 1 in FASTA (miRNA):
Sequence 2 in FASTA (mRNA):
maximum score
maximum mismatches maximum gaps
maximum consecutive mismatches no mismatches from base to base
have maximum mismatches from base to base
allow G:U wobble ? maximum G:U wobble
a G:U wobble means mismatches
match score mismatch score
G:U match score X / N mismatch score
gap-open score gap-extend score
    Try example      remove sequence