EST Database of Cotton

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