Biomedical Engineering Reference
In-Depth Information
website address
Algorithm
Method
Conservation
Website
Data retrieval
miRanda
Targets scored using sequence alignment,
site location within UTR
thermodynamics
Y
http://www.microrna.org
Search by transcript or
miRNA
PicTar
Predict targets for multiple miRNAs
(coexpression), targets scored on
complementarity, free energy threshold,
calculation of probabilities using HMM
Y
http://pictar.mdc-berlin.de/
Search by transcript or
miRNA
Diana-microT
miRNA driver sequence complementarity,
free energy binding applied to targets
with perfect complementarity
Y
http://diana.cslab.ece.ntua.gr/microT/
Search by transcript or
miRNA
TargetScan
Context scoring based on seed match,
thermodynamic stability, AU
composition
Y
http://www.targetscan.org/
Search by transcript or
miRNA
TargetScanS
6 nt seed match with adenosine at miRNA
position 1
+
calculation of context score
Y
http://www.targetscan.org/
Search by transcript or
miRNA
PITA
Determines free energy of target
accessibility of target along with duplex
formation energy
Y
http://genie.weizmann.ac.il/pubs/mir07/
mir07_prediction.html
Search by transcript or
miRNA or sequence
RNAhybrid
Identifies targets using thermodynamic
calculations requiring matches to the
seed region. Calculates significance of
target using a shuffled sequence
Y
http://bibiserv.techfak.uni-
bielefeld.de/rnahybrid/
Download program
Windows, Mac or Linux
RNA22
Species specific identification of targets via
alignment of variable length motifs and
thermodynamic assessment of “hotspots”
N
http://cbcsrv.watson.ibm.com/rna22.html
miRNA and mRNA
Sequence search
mirWalk
Target identification across mRNA, initial
identification of seed binding and
extension of alignment until mismatch
located
Y
http://www.umm.uni-
heidelberg.de/apps/zmf/mirwalk/index.html
Search by transcript or
miRNA
HOCTAR
Target identification through combination
of gene expression analysis and
traditional target prediction algorithms
Indirect through
overlap with
other
http://hoctar.tigem.it/index.php
Search by transcript or
miRNA
Search WWH ::
Custom Search