请问有什么软件可以筛选出序列中的hairpin structure??
丁香园论坛
665
就是在一篇文章中他们从一个序列数据库中筛选可能的miRNA,第一步是筛选可能的带hairpin的miRNA的precusor。他使用的是一个perl编辑的程序，可是肯定不会共享，看到其他的文章也是用了自己的程序，请问有没有免费的现成的程序可以用？？？？
文章在下面！！！
The Arabidopsis genome version 3 and the O. sativa genome
released by The Institute for Genome Research (TIGR) on 22
July 2002 [49] and 24 January 2003 [50], respectively, were
used for the present study. Intergenic regions of both the A.
thaliana and the O. sativa genomes were extracted according
to the annotations provided by TIGR. A scanning algorithm
implemented in the Perl programming language was used to
search for possible hairpin structures within each intergenic
sequence in A. thaliana. The method inspects each successive
21-nucleotide query window in each intergenic region, with
two nucleotide increments, and searches for downstream
complementary sequences with up to 25% mismatches. We
restricted the distance from the last base of the forward query
sequence and the first base of the downstream complementary
pairing sequence to a minimum of 10 nucleotides and a
maximum of 150 nucleotides (loop length). For
文章在下面！！！
The Arabidopsis genome version 3 and the O. sativa genome
released by The Institute for Genome Research (TIGR) on 22
July 2002 [49] and 24 January 2003 [50], respectively, were
used for the present study. Intergenic regions of both the A.
thaliana and the O. sativa genomes were extracted according
to the annotations provided by TIGR. A scanning algorithm
implemented in the Perl programming language was used to
search for possible hairpin structures within each intergenic
sequence in A. thaliana. The method inspects each successive
21-nucleotide query window in each intergenic region, with
two nucleotide increments, and searches for downstream
complementary sequences with up to 25% mismatches. We
restricted the distance from the last base of the forward query
sequence and the first base of the downstream complementary
pairing sequence to a minimum of 10 nucleotides and a
maximum of 150 nucleotides (loop length). For
