Analysis # 5 - Nabeel Siddiqui nhs256 Bio 206L Wed....

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Nabeel Siddiqui nhs256 Bio 206L Wed. 9:00-1:00 (49530) 2/24/2010 Bioinformatics and Bacterial Transformations Exercise # 5: Analysis 1. Bioinformatics and its resources are heavily rooted in the life sciences because they offer a range of computational tools needed to evaluate and analyze biological data. The large amounts of biological data such as gene sequences and amino acid sequencing for each individual organism can be searched up and analyzed from the database. The algorithm BLAST or Basic Local Alignment Search Toll allows us to compare biological patterns such as amino acid sequences between two separate organisms. These tools allow for the comparison of the two separate sets of biological sequences from two separate organisms. This can be done by simply searching up the wanted organism from the BLAST database and finding the resulting Amino Acid sequence. In the details section the individual amino acids can be located and compared with a different organism of a similar sequence. This information can be used to find the subtle differences in amino acid sequences between two organisms. Other programs such as MEGA 4 or ClustalW can actually analyze and construct phylogenetic trees from making pair wise alignments within protein sequences of different organisms. It works by computing the similarities and differences in the amino acids and then converting them into a distance matrix which in turn helps in diagramming the corresponding phylogenetic tree. 2. In the graphical view on the BLAST website, you are able to see the Name of the proteins which are represented by the different color lines shown on the graph. These lines are also color coordinated to match the number of alignments. For instance you can see the length of a particular amino acid sequence in the graphical view. In the descriptive view you can see the accession #, the score bits, the E-value as well as where the protein is found in the organism. When you click on the individual lines, the actual amino acid sequence for the protein in question shows up. Also in the descriptive view, you have the subject line, the query line and the middle line which gives a format on which you can compare the differences in two amino acid sequences. One is usually compared to another
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sequence of a similar organism. The advantages of the graphical view are that they provide a general overview of an organism and its protein location and also gives a few points of data such as the E-value as well as the accession number. The disadvantage of the graphical view is that the individual differences in amino acid sequences cannot be seen. However an advantage of the descriptive view is that the differences in the amino acid sequences can be compared with a subject line which corresponds to the amino acid sequence of a similar organism. The
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This note was uploaded on 01/25/2011 for the course BIO 206L taught by Professor Unknown during the Spring '08 term at University of Texas at Austin.

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Analysis # 5 - Nabeel Siddiqui nhs256 Bio 206L Wed....

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