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

2. To learn the tools of Bioinformatics Motivation Discovered Or
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
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 DAYS1 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
New Born Sequence
Total length
New Born Sequence
Total length
New Born Sequence
Total length

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 New 2229 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 Another one 2596
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 My stopping Point – 3218!! 8 271
BPHSe.AOIX3287-b2
Length - 894 3
266
My stopping Point – 3218!!

10. Investigation Open Reading Frames
We Have 3

11. NCBI Blastn - Freshwater metagenome 40753668
Blastx - Environmental sample proteins
gb|EDA | hypothetical protein GOS_ [marine metagenome]
gb|ECZ | hypothetical protein GOS_ [marine metagenome]
gb|ECZ | hypothetical protein GOS_ [marine metagenome]
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
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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