Week+of+10-4-09

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I went to Stepan Hall again, and I spoke with Dr. HG in more detail about bioinformatics itself and the available projects. Again leaving the options open for future decisions, I was tasked with looking at more of the tools commonly used in bioinformatics projects. While it may seem as though we are being hesitant on project selection, this is not the case. After all, there are certain tools that are necessary virtually regardless of which specific project that I choose, and it is better to have a sampling of these and to surmount the learning curve before getting carried away. There is plenty of time for that later. But back to the task at hand. I was first given a tour of the NCBI (National Center for Biotechnology Information) website (found here ) by Dr. HG, and briefly familiarized myself with the site and its layout. I was tasked with finding the protein that an amino acid sequence coded for, and what species it belonged to. This is the sequence:  code MRFLAATFLLLALSTAAQAEPVQFKDCGSV DGVIKEVNVSPCPTQPCQLSKGQSYSVNVT FTSNIQSKSS KAVVHGILMGVPVPFPIPEPDGCKSGINCP IQKDKTYSYLNKLPVKSEYPSIKLVVEWQL QDDKNQSLFC WEIPVQIVSHL

code

I used the search options of the NCBI site to look around for a suitable database to search. Remembering the previous bioinformatics student's page, I eventually settled on the BLAST database. BLAST (which stands for Basic Local Alignment Search Tool) is a database and search engine which contains the genomes of many species, as well as the proteins associated with them. The "tool" part comes into play when a search is executed, as it compares the search to the database and makes an extensive list of customizable comparisons. As I had an amino acid sequence, I followed the protein BLAST link. It brought me to the query sequence page, found here. I copied the sequence into the search window, keeping all of the options standard. This brought me to the rather lengthy result page, most of which was simply unfamiliar to me. Fortunately, I did not need to know much. I found the "Organism Report" option after following the "Taxonomy Report" and selected it, bringing me to this image:

Clearly, the most prominent result is that the sequence is from humans, and is involved in Nieman-Pick disease. This is logical in retrospect, as the previous student's page makes many references to the NPC2 proteins.