Bioinformatics 471

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

I just want to say that through this semester I have learned tremendously how to analyze data and think outside the box.  I enjoyed this class tremendously since it allowed me to work at my own pace and explored things with help.  I feel that I was not pressured in learning the materials in a set amount of time but can take it slow if I so choose.  I enjoyed it greatly hope everyone a wonderful break.

I continued to look for mRNA reference sequence of other species.  Ramsey helped me last week to find the correct one.  There are a lot of provisional and model RAI1 from other species.  I also found two articles about RAT1 that has to do with RAI1 in rat.  I thought this was interesting but disappointing that I could not access the entire paper but could only read the abstract.  Overall, the project is going well

I am working on Chromosome one of all 10 subjects. I am mainly looking the same mutations found in chromosome one of different patients. I work with excel and it was very frustrated because the excel was not meant to be for the work Stephen did. I used UCSC genome browser to get more information about the mutations. I thought UCSC would have information on all the mutation because Stephen post the link to it however i was unable to find information for some of the mutation. What i found how exactly i did the work are in my paper. Overall i think this paper wasn’t that bad.
Fez

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.

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.

A.)Begin SMS project

B.) I finally have a vague idea what to do on this project.  I was planning on doing the proposed 1B –> looking at all the chromosomes of an individual or 3 –> drag tree of different species that have RAI1 relative to human

A. Here is my plan for my project. My primary tool will of course be biology workbench. The objective of the project will be to see how conserved the RAI1 gene is between a great number of species phylogenetic trees will be consructed and comparisons will be made, of course the greatest challenge of this project will be finding all of the sequences that need to be inputted into biology workbench, but I have a few plans. My initial search will involve blast, but not just the NCBI blast, I will blast through the biology workbench because it provides a much wider variety of options, including allowing me to search for sequences within the Protein database, something that I was having alot of trouble with before. There are also other ways that a sequence can be found. I can use wormbase to find the sequence within the nematode c. elegans. From workbench I tried to use the Ndjinn multiple database search and I searched for RAI1, this didn’t seem to work, I think your supposed to actually input a sequence and then click on all the organisms that you want to see that specific sequence for, this seems like the quickest most effective way to find all the sequences for the RAI1 gene.  http://www.ncbi.nlm.nih.gov/nuccore/NG_0… This is the linkt o the FASTA sequence of the RAI1 gene, this is the sequence that I inputted into DJinn!!! EXCiting!! I’m not really sure if its actually going to ever load on my computer, the RAI1 gene sequence is really really long, and Djinn searches through multiple genomes of multiple organisms to try and find a match!!! I Think instead of using the whole sequence I will try to use just a portion of it to say if any matches come up. I think that this Djinn tool has alot of potential to find certain sequences within a great number of organisms. I don’t think my computer actually can do it because it still not working, I will try it tommorow when I have access to a school computer. O and of course, to create the phylogenetic tree, I will use the same techniques as before!!!

I would like to look more closely at the currently published structure of RAI1 as presented in the  Toulouse 2003 paper.  This paper uses informatics techniques such as comparing the gene structures of related organisms and combining ESTs and partial mRNAs from NCBI, as well as wet lab techniques to create a structure of the human RAI1 gene.  The Elsea lab, however, suspects this structure to be incorrect.  I would like to closely examine the techniques and logic flow leading the authors to their final conclusion, focusing specifically on holes in the logic and possible alternative explanations of the data presented.  I will also include the reasoning that led the Elsea lab to suspect that this structure is in fact incorrect.  If time permits, I would also like to research what is currently known about the function of RAI1 in the human body.

Topics, Concepts & Skills:

Overall
An idea of the scope and limitations of bioinformatics.
An ability to blog/make a website, create links and imbed images/videos.

Muscular dystrophy
History of muscular dystrophy and related diseases.
Understanding of role of cytogenetics and bioinformatics in identifying the Dystrophin. This includes chromosome banding/ideograms. Cellular role of Dystrophin in relation other proteins that cause DMD and other dystrophies, including LGMD. Relation of severity of genetic defect to disease phenotypes. Other assays used in studying muscular dystrophies.
Use of OMIM to learn about locations and functions of various components of the Dystroglyan Complex.
Experience with PDB files of protein structures.

The Human Genome Project and DNA sequencing
Understanding of the process of Genome Sequencing and Annotation, including new developments that have accelerated sequencing.  Topics studied include base calling/issues with sequence quality and coverage, assembly of BAC clones into a Contig, finishing, annotation.

Appreciation of the historical significance of the Human Genome Project and the international collaborative nature of the project. Role of Hierarchical vs. Whole-genome sequencing in the final project. Read and wrote about the beginning sections of the HGP’s 2001 Nature Paper.

Touched upon or used PHRED, PHRAP, Sequencher.

Familiarity with the work of Craig Venter on the Human Genome Project and the JCVI’s recent research directions, including the Global Ocean Sampling Expedition, Marine Microbe Genome Sequencing Project, Synthetic Biology for microbes and vaccines, identification of entire new families of protein domains.

Gene Detection and Genome Annotation
Hands on experience with Gene Calling and Annotation (finding related genes), using the bacteriophage Eagle genome.

Dot plots and the role of visual analysis in understanding genomes.

Differences in prokaryotic vs. eukaryotic genes and the effect of those differences on Gene Detection. Methods used in gene annotation.

HIV Project
Read and understand primary literature. Explained a primary paper in a journal club format.
Developed and explored a unique bioinformatics question using original data from the HIV paper.
Some experience with new software, its power, and its limitations. The software includes Biology Workbench, Biology Student Workbench, SWAMI, ClustalW, and in one case MEGA4. Other tools used include Align, Grol4, MView, MEME.
Built phylogenic trees. Learned that file formats can make or break you.
Presented unique project in a class presentation and as a paper.

Multiple Alignments and Phylogenic Trees
Learned about different types of trees, their parts and what they can tell you. Touched upon how to pick the correct sequence to use in making a tree (synteny & orhtologs), theoretical approaches, synonymous and non-synonymous sites. Using fast-mutating vs. highly conserved sequences.

SMS Project
Met a graduate student author of a bioinformatics paper. Learned about the complex disease Smith-Magenis Syndrome.
Learned about clinical features of SMS and diagnostic methods related to bioinformatics. Journal Club of an original paper using the array comparative genomic hybridization technique. Analysis/critique of results and data presentation.

Original Project using data from SMS paper or RAI1 gene sequences. Presented in paper format.

Genome structure: repeats, SNPs, CNVs.