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Knowledge of Hot Springs

Join the Bioinformatics journey of discovery at the VCU Symposium, learning valuable tools and techniques, including sequence analysis, overlap identification, and open reading frames exploration. Trace the steps of putting together the molecular puzzle pieces and discovering new insights in bioinformatics research. Explore NCBI databases, Blastn and Blastx analyses, and advanced gene prediction methodologies using GeneMark. Enhance your understanding of molecular biology through hands-on experience and unlock the mysteries hidden within genetic sequences.

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Knowledge of Hot Springs

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  1. Knowledge of Hot Springs VCU Symposium on Applied Bioinformatics Deborah Hamill May 6, 2009

  2. Overall Goal To learn the tools of Bioinformatics Motivation Discovered Or At least figure out BioBIKE

  3. Journey of Discovery • Many Hours • Lots if phone calls • Backing up • Questioning • Camping in the library • FINALLY, put it together

  4. Putting the Puzzle Together Putting the Puzzle Together Putting the Puzzle Together Putting the Puzzle Together Putting the Puzzle Together Putting the Puzzle Together Putting the Puzzle Together Putting the Puzzle Together Putting the Puzzle Together Day 1 Day 1 Day 1 Day 1 Day 1 Day 1 Day 1 Day 1 My very own sequence. My very own sequence. My very own sequence. My very own sequence. My very own sequence. My very own sequence. My very own sequence. My very own sequence. My very own sequence. OctHSe.APNO3619-b2 OctHSe.APNO3619-b2 OctHSe.APNO3619-b2 OctHSe.APNO3619-b2 OctHSe.APNO3619-b2 OctHSe.APNO3619-b2 Length - 928 Length - 928 Length - 928 Length - 928 Length - 928 Found a Start codon at 825, nothing else

  5. Continuation of DAYS Continuation of DAYS Continuation of DAYS Continuation of DAYS Continuation of DAYS Continuation of DAYS Continuation of DAYS Continuation of DAYS Continuation of DAYS Continuation of DAYS Continuation of DAYS Continuation of DAYS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 660 660 660 660 660 660 660 660 660 660 660 660 660 660 660 660 660 660 660 660 660 915 915 915 915 915 915 915 915 915 915 915 915 915 915 915 915 915 915 915 915 OctHSe.APNO3619-b2 overlaps with OctHSe.ATYB6681-g2 OctHSe.APNO3619-b2 overlaps with OctHSe.ATYB6681-g2 OctHSe.APNO3619-b2 overlaps with OctHSe.ATYB6681-g2 OctHSe.APNO3619-b2 overlaps with OctHSe.ATYB6681-g2 OctHSe.APNO3619-b2 overlaps with OctHSe.ATYB6681-g2 OctHSe.APNO3619-b2 overlaps with OctHSe.ATYB6681-g2 OctHSe.APNO3619-b2 overlaps with OctHSe.ATYB6681-g2 OctHSe.APNO3619-b2 overlaps with OctHSe.ATYB6681-g2 OctHSe.APNO3619-b2 overlaps with OctHSe.ATYB6681-g2 OctHSe.APNO3619-b2 overlaps with OctHSe.ATYB6681-g2 OctHSe.APNO3619-b2 overlaps with OctHSe.ATYB6681-g2 OctHSe.APNO3619-b2 overlaps with OctHSe.ATYB6681-g2 OctHSe.APNO3619-b2 overlaps with OctHSe.ATYB6681-g2 OctHSe.APNO3619-b2 overlaps with OctHSe.ATYB6681-g2 OctHSe.APNO3619-b2 overlaps with OctHSe.ATYB6681-g2 1 1 1 1 1 1 1 1 1 1 258 258 258 258 258 258 258 258 258 258 258 258 964 964 964 964 964 964 1635 1635 New Born Sequence Total length - 1635 New Born Sequence Total length - 1635 New Born Sequence Total length - 1635 New Born Sequence Total length - 1635

  6. Continuation and DAYS No new reading frames but my first overlap 1635 1325 903 595 OctHSe.ATYB4385-b2 Total length 935 With a reading frame!!

  7. More overlap No new reading frames but another overlap 1635 1325 903 595 OctHSe.ATYB4385-b2 Total length 935 With a reading frame!! New 2229 But wait another addition… 1700 2229 1 530 BPHSe.AOIX3287-b2

  8. Once More No new reading frames but another overlap 1635 1325 903 595 OctHSe.ATYB4385-b2 Total length 935 With a reading frame!! 1700 2229 Another one 2596 1 530 BPHSe.AOIX3287-b2

  9. FINALLY!!CONTIG MAP 8 271 BPHSe.AOIX3287-b2 Length - 894 3 266 My stopping Point – 3218!!

  10. InvestigationOpen Reading Frames We Have 3

  11. NCBI • Blastn - Freshwater metagenome 40753668 • Blastx - Environmental sample proteins gb|EDA91841.1| hypothetical protein GOS_1913245 [marine metagenome] 37.7 1.8 gb|ECZ09141.1| hypothetical protein GOS_2243444 [marine metagenome] 36.2 5.1 gb|ECZ34061.1| hypothetical protein GOS_2200681 [marine metagenome] 35.8 6.7 Additional find: Chain A, Crystal Structure Of The Receptor Protein Tyrosine Phosphatase

  12. Gene Mark • Parse predicted by GeneMark.hmm 2.4 • PROKARYOTIC (Version 2.6r) Model organism: Escherichia_coli_K12 Predicted genes Gene Strand LeftEnd RightEnd Gene Class • + <2 478 477 2 • + 478 846 369 2 • + 846 938 93 1 • + 958 1167 210 2 • + 1151 1552 402 2 • + 1588 2241 654 2 • + 2232 2801 570 2 • + 2838 3170 333 2

  13. The End of My Story • A little is better than nothing • Working with sequence is a labor of love • BioBike can be your friend Thank You

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