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Computational Bioinformatics: Computational Bioinformatics: Software and Databases Software and Databases Jason T. L. Wang, Professor Bioinformatics Program and Computer Science Department New Jersey Institute of Technology

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Computational Bioinformatics: Computational Bioinformatics: Software and Databases Software and Databases

Jason T. L. Wang, Professor

Bioinformatics Program and Computer Science Department New Jersey Institute of Technology http://web.njit.edu/~wangj

Work supported by NSF grant IIS-0707571

Presentation for NSF-Sponsored C2PRISM Program

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Outline

Introduction to Bioinformatics
Introduction to Computational RNA

Genomics (Our Current Project)

RNA Informatics Tools
RNA Databases
Bioinformatics Center
Conclusion and Future Work

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Gene:

Genetic information-containing elements
Distributed to each cell when cell divides
Made of deoxyribonucleic acid --DNA

Gene:

Genetic information-containing elements
Distributed to each cell when cell divides
Made of deoxyribonucleic acid --DNA

Gene Structure:

Promoter
Start codon
Introns
Exons
Stop codon
etc

Gene:

Transcription : DNA to RNA
RNA Splicing: Remove Intons--mRNA
mRNA translation--Protein

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Exon 1 Intron 1 Exon 2 Intron 2 Exon 3 CCCTGTGGAGCCACACCCTAGGGTTGGCCAATCTACTCCCAGGAGCAGG GAGGGCAGGAGCCAGGGCTGGGCATAAAAGTCAGGGCAGAGCCATCTAT TGCTTACATTTGCTTCTGACACAACTGTGTTCACTAGCAACTCAAACAG ACACCATGGTGCACCTGACTCCTGAGGAGAAGTCTGCCGTTACTGCCCT GTGGGCAAGGTGAACGTGGATGAAGTTGGTGGTGAGGCCCTGGGCAGGT TGGTATCAAGGTTACAAGACAGGTTTAAGGAGACCAATAGAAACTGGGC ATGTGGAGACAGAGAAGACTCTTGGGTTTCTGATAGGCACTGACTCTCT CTGCCTATTGGTCTATTTTCCCACCCTTAGGCTGCTGGTGGTCTACCCT TGGACCCAGAGGTTCTTTGAGTCCTTTGGGGATCTGTCCACTCCTGATG CTGTATGGGCAACCCTAAGGTGAAGGCTCATGGCAAGAAAGTGCTCGGT GCCTTTAGTGATGGCCTGGCTCACCTGGACAACCTCAAGGGCACCTTTG CCACACTGAGTGAGCTGCACTGTGACAAGCTGCACGTGGATCCTGAGAA CTTCAGGGTGAGTCTATGGGACCCTTGATGTTTTCTTTCCCCTTCTTTT CTATGGTTAAGTTCATGTCATAGGAAGGGGAGAAGTAACAGGGTACAGT TTAGAATGGGAAACAGACGAATGATTGCATCAGTGTGGAAGTCTCAGGA TCGTTTTAGTTTCTTTTATTGCTGTTCATAACAATTGTTTTCTTTTGTT TAATTCTTGCTTTCTTTTTTTTTCTTCTCCGCAATTTTTACTATTATAC TTAATGCCTTAACATTGTGTATAACAAAAGGAAATATCTCTGAGATACA TTAAGTAACTTAAAAAAAAACTTTACACAGTCTGCCTAGTACATTACTA TTTGGAATATATGTGTGCTTATTTGCATATTCATAATCTCCCTACTTTA TTTTCTTTTATTTTTAATTGATACATAATCATTATACATATTTATGGGT TAAAGTGTAATGTTTTAATATGTGTACACATATTGACCAAATCAGGGTA ATTTTGCATTTGTAAATTTTAAAAAATGCTTTCTTCTTTTAATATACTT TTTTGTTTATCTTATTTCTAATACTTTCCCTAATCTCTTTCTTTCAGGG CAATAATGATACAATGTATCATGCCTCTTTGCACCATTCTAAAGAATAA CAGTGATAATTTCTGGGTTAAGGCAATAGCAATATTTCTGCATATAAAT ATTTCTGCATATAAATTGTAACTGATGTAAGAGGTTTCATATTGCTAAT AGCAGCTACAATCCAGCTACCATTCTGCTTTTATTTTATGGTTGGGATA AGGCTGGATTATTCTGAGTCCAAGCTAGGCCCTTTTGCTAATCATGTTC ATACCTCTATCTTCCTCCCACAGCTCCTGGGCAACGTGCTGGTCTGTGT GCTGGCCCATCACTTTGGCAAAGAATTCACCCACCAGTGCAGGCTGCCT ATCAGAAAGTGGTGGCTGGTGTGGCTAATGCCCTGGCCCACAAGTATCA CTAAGCTCGCTTTCTTGCTGTCCAATTTCTATTAAAGGTTCCTTTGTTC CCTAAGTCCAACTACTAAACTGGGGGATATTATGAAGGGCCTTGAGCAT CTGGATTCTGCCTAATAAAAAACATTTATTTTCATTGCAATGATGTATT TAAATTATTTCTGAATATTTTACTAAAAAGGGAATGTGGGAGGTCAGTG CATTTAAAACATAAAGAAATGATGAGCTGTTCAAACCTTGGGAAAATAC ACTATATCTTAAACTCCATGAAAGAAGGTGAGGCTGCAACCAGCTAATG CACATTGGCAACAGCCCCTGATGCCTAATGCACATTGGCAACAGCCCCT GATGCCTATGCCTTATTCATCCCTCAGAAAAGGATTCTTGTAGAGGCTT GATTTGCAGGTTAAAGTTTTGCTATGCTGTATTTTACATTACTTATTGT TTTAGCTGTCCTCATGAATGTCTTTTC Promoter Start Codon Exon 1 Exon 2 Exon 3 Stop Codon Intron 1 Intron 2 Start Codon Stop Codon Start Codon Stop Codon Start Codon Stop Codon Transcription Splicing( intron removal) Gene pre-mRNA mRNA

Gene Structure and Gene Expression

Acceptor site Acceptor site Donor site Donor site Splicing( RNA rejoining) Donor site Donor site Acceptor site Acceptor site Translation Protein

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Computational RNA Genomics

Biochemical and genetic

studies have demonstrated many functions associated with the UTRs in mRNAs.

Unlike proteins, RNA

sequence search is insufficient for detecting similarity.

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Sequence Similarity vs. Structural Similarity

>NM_000032 UUCGUUCGUCCUCAGUGCAGGGCAACAGGA ((((((.(((((......)))))))).))) >NM_014585 CAACUUCAGCUACAGUGUUAGCUAAGUUUG ((((((.(((((......)))))))).)))

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RSmatch and RADAR

(BMC Bioinformatics 2005) (Nucleic Acids Research 2007) Alignment of two RNA secondary structures where the local matches found by RSmatch are in green.

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Multiple Structural Alignment

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GLEAN-UTR Database

(BMC Genomics 2008)

Use RADAR, hierarchical clustering and Gene

Ontology to mine RNA motifs in the UnTranslated Regions (UTRs) conserved between human and mouse orthologs in multiple genes sharing common biological pathways.

GLEAN-UTR DB contains 90 RNA motifs

(structure groups) from 698 genes. Top two motifs are Iron response element (IRE) and histone 3’- UTR stem-loop structure. http://datalab.njit.edu/biodata/GLEAN-UTR-DB/

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Conclusion

We have developed a warehouse of

informatics tools and databases for RNA genomics.

We want to invite high school students to
ur research team to conduct interesting

research (Liberty Science Center Model)

Contact Dr. Jason Wang (wangj@njit.edu)
http://web.njit.edu/~wangj