| Name: |
miRNA |
| Version(s): |
targetscan -- 1.0beta
miranda --1.0b |
| Category: |
RNA analysis, Sequence analysis, Bioinformatics |
| Author(s)/Vendor(s): |
targetscan: Ben Lewis
miranda: AntonEnright, Bino John, Chris Sander and Debora Marks
(mirnatargets@cbio.mskcc.org - to all authors) |
| Program Description: |
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 |
| Computer platform(s): |
IRIX64 |
| Location: |
targetscan: /abcc/apps/IRIX64/targetscan/targetscan
miranda: /abcc/apps/IRIX64/miRanda-1.0b/bin/miranda and /usr/local/bin/miranda |
| Access: |
for web use:
http://www.abcc.ncifcrf.gov/app/htdocs/appdb/drawpage.php?appname=miRNA
for commandline use:
log onto ncisgi. find the program from its "Location" and run it. |
| Documentation: |
/app/htdocs/appdb/appinfo.php?appname=miRNA |
| Web Site: |
/app/htdocs/appdb/drawpage.php?appname=miRNA |
| ABCC Contact Person: |
Bob Stephens
(301)846-5787
bobs@ncifcrf.gov
Jigui Shan
(301)846-5157
shanj@ncifcrf.gov
|
| Created By: |
Jigui Shan |
| Created Time: |
|
| Updated By: |
Jigui Shan |
| Updated Time: |
2006-01-11 |
