Applications of Hidden Markov Models in the Avian/Mammalian Genome Comparison Christine Bloom Animal Science College of Agriculture University of Delaware

Conclusions of Project  Have I accomplished what I set out to do? –Do the HMMs that I created identify chicken IL-2 and IL-15 sequences? –Do the modified HMMs I created give better scores for chicken sequences than the original profiles without lower the scores of sequences of the other family members? –Did I find a new signature suitable for identifying all members of the IL-2 family?

Conclusions of Project Cont.  By running my profile HMM against a small database through SAM-T99 I found: –For Il-2: 87 matches of which nearly one quarter were sequences that were not used in the making of the profile. 5 of these sequences were avian sequences. –For Il-15:24 matches of which 6 were sequences not used in the making of the profile. Of these 3 were Avian sequences.

Conclusions of Project Cont.  The fact that more avian sequences are detected by my adjusted profile than with the original pFAM profiles leads me to believe that the scores are better for the adjusted profiles.  HMM provided by SAMT99 has no key for determining identity of positioning.

Conclusions of Project Cont.  A new signature identifying Il-2 in all species including avian was not found. –Few conserved regions among all sequences were found in the finale profile. –Choosing to identify any of these regions as “The Signature” may cause problems if, in reality, other unknown sequences do not have that region.