Notebook

Bioinformatics has been an interesting learning process. I definitely learned alot about the different databases, some are more useful than others. Overall I found bioinformatics is more of an analyzing tool than anything else. I enjoyed this class a lot but I am soooooo happy the semester is over!!! Hope everyone has an awesome winter break

Tags: bioinformatics, informatics, Lab Notebook

I worked on the SMS project today. I found the full nucleotide sequence and amino acid sequence for RAI1 (homosapiens). I looked through ncbi for other organism RAI1 sequences but they seem to be a lot shorter than the human. I also submitted the a.a. to PSIPRED for the predicted secondary structure. Looking at  the results they sent me, there does not seem to be a lot of helices or beta sheet. I’m going to look for another program to predict secondary structure. I also looked at RCSB for the crystallized structure, however it seems that its only a portion of the RAI1 protein or the a.a. sequence I obtained is wrong. I’ll update my findings later when I figure it out.

Tags: bioinformatics, informatics, Lab Notebook

We have been presenting Steven Williams paper for the past two class days. I found the presentations helpful in explaning the paper’s method. I thought Steven’s paper was a poor reflection of his work. His presentation to our class was a better explanation than his paper did about his methods. I think Steven’s research is good, I wished he had reviewed his paper and possibly modified it before submission. I also had a problem with his choice of words for pathogenic and nonpathogenic CNV as Calvin has mentioned. I also would like to know more about RAI1 and its function.

Tags: bioinformatics, informatics, Learning Notebook

This week we had HIV project presentation. Everyone’s presentations were good. I found Calvin’s topic very interesting. His approach to look at the possible protein structure of the VP3 and to find possible conserved secondary motifs very interesting. I think if I continued with my project I would have ended my project looking at possible conserved protein motifs that may be important for the HIV env gene to infect T cells. I think it would be a really cool lab project to make point mutations of the amino acid sequence in the proposed conserved sencondary motifs to see if it would affect the HIV VP3 proteins ability to infect CD4 T cells. I also liked Chris’ project on the drug abuse of the subjects in the Markham paper. His results that the increase in drug use increased in CD4 Tcell count reduction. The relationship of rapid progression and greatest drug use show that the environment of the subject have an influence on the subjects immune system. I also liked that Chris’ project clarified that the subjects in the Markham paper did not take any antiviral drugs since it was unstated in the paper and left the reader guessing. Overall the results found from all the projects were intresting in that they revealed different aspects of the Markham project that was not included in the paper.

Tags: bioinformatics, informatics, Lab Notebook, Learning Notebook

Steve’s presentation on his study on SMS at the Elsea Lab was complete on SMS features. I learned what SMS is. I found the diagnosis of SMS very interesting since its very specific. Steve and his lab used aCGH to look at the whole genome to evaluate the RAI1 gene. I also found Steve’s hypothesis that people functioning in normal society may have polymorphisms and may be a contributing cause to people who may have a mild development delay or social problems.

What I enjoyed most of Steve’s visit was talking about graduate schools. He mentioned several good questions to ask labs that one may be applying to that I would not have thought to ask, such as do you like your mentor. lol.

I’m sorta looking forward to analyze the data.

Tags: bioinformatics, informatics, Lab Notebook, Learning Notebook

Molecular Evolutionary Genetics Analysis (MEGA 4) is a free program. It is really useful for making phylogenetic trees and aligning sequences. I think its more useful for nucleotide analysis than amino acid analysis.In the program you can translate the nucleotide sequence or untranslate the amino acid sequence. MEGA 4 can do clustal alignment and it shows the constant sites, variable sites, and parsimony sites. In the alignment you can also blast a sequence or go into genbank. It also has sequencher base edit. The most useful part of MEGA 4 is the different phylogenetic tree that you are able to make. I used MEGA 4 to make phylogenetic trees of the subjects 5,7,and14. I initially made a.a. phylogenetic trees, but then I started to play around with the options and found that I could draw a tree of nonsynonymous or just synonymous mutations between the sequences. They also had the options for neighbor joining, bootstrapping, minimum evolution, and maximum parsimony.  I used Neighbor Joining to make my trees the same way as the Markham paper. Once the tree was made I chose where I wanted to root my tree and then colored different branches to mark the various visits. There are other drawing tools for the asthetics of the trees but I haven’t really used them. The trees I made for nucleotide difference was the same as the Markham paper. I also made trees of nonsynonymous mutations. There was a decrease in diversity, as expected, and the overall shape was the same. I think MEGA4 is rad since I got the figures I wanted and I could save my data and export it.

Tags: bioinformatics, informatics, Lab Notebook

• My topic is going on the nonsynonymous mutations of the env gene sequence that the Markham paper looked at. I will be specifically looking at the nonsynonymous mutational changes of the nucleotides in subject 1 5 and 7.
• My question is to see if the elimination of the synonymous mutations will change how diverse the strain is from the results found in the paper and how far clones diverge from the V1-1.
• I plan to make a Phylogenetic tree and compare it to the paper’s Phylogenetic tree. The easiest way I think to make the tree is to compare the a.a. sequences of all the visits for each subject I am planning to analyze.
• The hardest thing is to figure out how to make a tree that compares all the sequences to the V1-1. I tried to form a phylogenetic tree but clustal does not let me choose a reference sequence.
• Next step would be to figure how to fix the problem.

Tags: bioinformatics, informatics, Lab Notebook

I guess I want to look at the nonsynonomous mutations of the HIV strains and possibly look at the strain diversity and divergence and possibly make a tree of only the nonsynonomous mutations, since synonomous produces are silent.

Tags: bioinformatics, informatics, Lab Notebook

SWAMI is awesome! all the database tools that you need are all there. It seems like it will make analyzing data a lot faster since the tools are all in one place and we wont have to go onto various websites. What a time saver this website will be. yay!

Tags: bioinformatics, informatics, Learning Notebook

Journal club was fun. I thought Thomas and Leah’s presentation was insightful, they graphed the data table and looked at the correlations. The 2 phylogenetic trees presentation fully explained their phylogenetic tree. I didnt realize that the line length indicated how many nucleotide mutations there were. Subject 7 was the most interesting in the phylogenetic tree presentation; It initially does not look like the other trees. When you compare figure 1 patient 7 graph to the phylogenetic tree the data both show the same thing, initially diversity is decreased and then increases towards the end, and divergence increases from every visit. The difference in subject 7 tree to the other tree might be that they tested the patient right when he/she seroconverted and the other subjects a little after they seroconverted that’s why towards later visits the tree starts to look like the other trees.

Tags: bioinformatics, informatics, Lab Notebook, Learning Notebook