Protein Gene BLAST

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         From previous lecture, we had learnt to use a search tool called Basic Local Alignment Search Tool (BLAST). BLAST finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance. In the previous lecture by Dr Azran, he taught us how to use BLAST for a protein gene. For example, we want to find the BRCA1 genes. We search the gene of BRCA1 for homo sapiens in National Centre for Biotechnology Information (NCBI). 

           Secondly, we make a comparison between the homo sapiens BRCA1 gene with other BRCA1 animal gene that is similar to human gene which are Pan troglodytes (chimpanzee), Rattus norvegicus (norway rat), Myotis lucifugus (little brown bat), Acinonyx jubatus (cheetah) and finally Dipodomys ordii (Ord's kangaroo rat). 

           Thirdly, the nucleotide sequence of the gene was downloaded from BLAST in FASTA format. From the nucleotide sequence in FASTA, we transfer it into CLC sequence viewer. Next, each sequence was selected and converted to protein sequence. After that, alignment was made for all sequence and a phylogenetic tree was produced in order to simplify all information gathered. From the phylogenetic tree made, all the gene compared is shown in simple diagram for any public viewer to understand.

 made by;
Amirul Ashraf   1612855
Ahmad Rabbani 1611535

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