ABCC : Applications Web Page

Applications Web Page Welcome to the ABCC Accessible Application Web Page.

From this page, you can get information about our scientific applications and databases. To get more information about any topic, or to run an application, click on any of the menu items on the left-hand side. Program with a tag "Run" is runnable. This site continues to grow, so come back often to check out the many accessible applications available here at the Advanced Biomedical Computing Center (ABCC).

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miRNA Analysis
miRNA
Targetscan is an algorithm for identifying microRNA target sites in UTR sequences. Given a miRNA and a database of UTR sequences, targetscan (1) searches the UTRs for segments of perfect Watson-Crick complementarity to bases 2-8 of the miRNA (numbered from the 5' end) - we refer to this 7 nt segment of the miRNA as the "miRNA seed" and UTR heptamers with perfect Watson-Crick complementary to the seed as "seed matches"; (2) extends each seed match with additional base pairs to the miRNA as far as possible in each direction, allowing G:U pairs, but stopping at mismatches; (3) optimizes basepairing of the remaining 3' portion of the miRNA to the 35 bases of the UTR immediately 5' of each seed match using the RNAfold program (Hofacker et al., ), thus extending each seed match to a longer "target site"; (4) assigns a folding free energy to each such miRNA:target site interaction using RNAeval (Hofacker et al.). During the folding process, targetscan disallows the microRNA sequences and UTR sequences from basepairing with themselves - this is to say that the only allowed pairings occur between opposite strands of the duplex. Target sites in which the 35 nt flanking region contains masked bases are discarded. miRanda: An miRNA target scanner that aims to predict mRNA targets for microRNAs using dynamic-programming alignment and thermodynamics
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