miRFinder Version 4.0 A freeware for microRAN prediction
For Windows 98/Me/NT/2000/XP and for Linux/FreeBSD/Solaris

Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, PR China
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MiRFinder is a high throughput and good performance computational pre-miRNA prediction tool. The tool was designed for genome-wise, pair-wise sequences from two related species. In our experiments, the MiRFinder has demontracted reasonably better sensitivity and speed comparing to similar tools.

New features proposed for pre-miRNA prediction
MiRFinder improved its performance of pre-miRNA prediction by utilize a set of novel features:
1.Correlation between mutation and secondary structure
Three types of mutations have slight changes of the secondary structure of pre-miRNA: mutations located in the loop region; mutations between A and G, U and C; and mutations that happen in the interrelated region of both arms that can not break the base-pairing. In pseudo pre-miRNA the disturbance of the secondary structure resulting from mutations is much higher than that of real miRNAs. This is a valuable feature for miRNA prediction.
2.Local secondary structure of pre-miRNA
The distribution of the loops is distinctly different between that of pseudo and real pre-miRNAs. We proposed a novel syntax to further elucidate the information of the secondary structure. Five symbols (“=”, “:”, “.”, “-“, “^”) were introduced into the syntax to represent the status (match, mismatch, etc.) of each nucleotide base pair in the stem region of the secondary structure predicted by miRfold. The new syntax focused on the information of every two adjacent symbols. The frequency of the14 possible combinations each combination defines a set of novel and useful features.

An actual example: Testing of the tool with a real genome in practical.
To test the performance of the tool, miRFinder was used to predict pre-miRNAs from Chicken/Human pairwised genome alignments. To show the superiority of miRNAfinder pre-miRNA prediction, comparison was done with miRscan (Lim et al., 2003) which is one of the most well-known and popularly used miRNA prediction software. Click here to download the results.

Discussion and conclusing
MiRFinder can be a better alternative of other miRNA discovery software.
We have targeted several purposes in developing this software: To provide a universally useful software for prediction of new pre-miRNAs in different species; To automatically process large amounts of genomic sequences locally; To find as many as possible pre-miRNA candidates; To be easily used by people who have little knowledge about the computational theory and processes used behind the scenes.
The test results showed that our program met these goals relatively well.