RNA Secondary RNA Secondary Structures: Structures: A Case Study - - PowerPoint PPT Presentation
RNA Secondary RNA Secondary Structures: Structures: A Case Study on A Case Study on Viruses Viruses Bioinformatics Senior Project Bioinformatics Senior Project John Acampado John Acampado Under the guidance of Dr. Jason Wang Under the
Bioinformatics Senior Project Bioinformatics Senior Project John Acampado John Acampado Under the guidance of Dr. Jason Wang Under the guidance of Dr. Jason Wang
Overview RSpredict JAVA RSpredict WebServer RNAstructure Cis-Regulatory
Virus Data Alignment Phylogenetic Tree RSpredict WebServer
Analysis / Conclusion Resources Contact Information
Secondary structure analysis of RNA in
Take various virus sequences that are cis-reg
Use both RSpredict and RNAstructure programs Phylogenetic tree shows distance and
Used to effectively predict the secondary structure Takes into account sequence variation Uses FASTA file format for input, outputs CT and Vienna
Machine Settings:
Microsoft Windows XP Service Pack 2 Intel Pentium M 1.59GHz, 512MB RAM
Link for RSpredict JAVA
RSpredict program also
Accepts the more
Output still in CT and
Link for RSpredict
Uses CT (Connectivity Table) from RSpredict to
Developed at the University of Rochester
Used for prediction and analysis of RNA
Link to RNAstructure
Region of RNA that is able to regulate the
Often on binding sites of one or more trans-
May be located in the promoter 5’ region, or the
Eleven viruses were used and analyzed for this
Gathered from RNA Families Database of
Sequences were chosen and entered manually Sequences of type “cis-reg” Sequences listed as virus within description All sequences chosen to have the ability to
Brief description and Rfam structure provided
RNA element found in 3’
Stimulates translation of
Contains at least two
Family represents
Thought to play important
May also be involved with
RNA element thought to
Critical for leader
Similar structures have
Thought to contain three
Structure of sequence
Primer binding site is
tRNA binds to site to
RNA element known as
Essential for viral
Found on U leader exon
Allows translation to
Thought to be necessary
Small hairpin structure
May play a role in RNA
Located in the 5’ terminal
Consists of two stem-loop
Disruption impairs both
Cis-acting regulatory
Located in protein coding
Essential for efficient viral
Found in 3’ UTR of
All loop structures
Deletion of stem loop
Alignment generated from Vienna sequences
ClustalW2 alignment tool used to align
ClustalW2 aligned all eleven sequences
Phylogenetic tree generated from Vienna output
Shows the distances of the sequences from
ClustalW2 tool from EMBL-EBI website Generated phylogenetic tree, with gaps turned
Ran RSpredict via WebServer on the same eleven
Identical results to JAVA, but with a friendlier interface No need to use command line interface, everything on
CT and Vienna files available for download, to then be
Side-by-side comparison of results on following slide
Side-by-side comparison of Webserver and JAVA RSpredict with identical results.
Identical results after CT file was input into RNAstructure to get sequence structure.
Average length and sequence identity correct when
Structure from RNAstructure does not match that of
RSpredict takes FASTA files as input and outputs CT
There are many similarities between Rfam and
Phylogenetic tree shows relationships between the
EMBL-EBI: http://www.ebi.ac.uk/ Rfam:
RNAstructure:
RSpredict:
Senior Project: http://web.njit.edu/~jsa4/SeniorProject/
John Acampado