Bioinformatics Links Directory : Functional RNAs

This section contains information on various functional RNAs. Included are tRNAs, non-coding RNAs, rRNAs and snoRNAs.

CrossLink - (Found July 2, 2008 )

Crosslink is a tool for visualizing pairwise sequence similiarity relationships determined using BLAST, Vmatch, and RNAhybrid. The nucleotide sequences and their relationships are displayed as nodes and links of a network, respectively. CrossLink can be useful for investigating potential interactions between microRNAs and their targets.
http://www-ab.informatik.uni-tuebingen.de/software/crosslink/webstart/welcome.html

miPred - (Found July 2, 2008 )

miPred (microRNA Predictor) can distinguish between real and pseudo microRNA precursors.
http://www.bioinf.seu.edu.cn/miRNA/

Non-Coding RNA database - (Found July 2, 2008 )

Non-translatable RNA transcripts that appear to work at the RNA level.
http://biobases.ibch.poznan.pl/ncRNA/

Rfam - (Found July 2, 2008 )

Database of structure-annotated multiple sequence alignments, covariance models and family annotation for a number of non-coding RNA families.
http://www.sanger.ac.uk/Software/Rfam/

RNAmmer - (Found July 2, 2008 )

RNAmmer predicts genes for ribosomal RNA (rRNA) in full genome sequences using hidden Markov models trained on data from the 5S ribosomal RNA database and the European ribosomal RNA database project.
http://www.cbs.dtu.dk/services/RNAmmer/

snoGPS - (Found July 2, 2008 )

snoGPS allows you to search for HACA snoRNA (small nucleolar RNA) genes in a genomic sequence
http://lowelab.ucsc.edu/snoGPS/

TFAM - (Found July 2, 2008 )

TFAM is a system to classify the function of tRNAs that is based on tRNA structural alignments.
http://tfam.lcb.uu.se/

tRNAscan-SE - (Found July 2, 2008 )

tRNAscan-SE allows you to search for tRNA genes in genomic sequence. (site hosted by Lowe Lab at UCSC)
http://lowelab.ucsc.edu/tRNAscan-SE/

tRNAscan-SE - (Found July 2, 2008 )

tRNAscan-SE allows you to search for tRNA genes in genomic sequence. (site hosted by Eddy Lab at WashU)
http://www.genetics.wustl.edu/eddy/tRNAscan-SE/