Bioinformatics+exercise.docx

Bioinformatics+exercise.docx - Name 3100 211 Genetics Fall...

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Name: 3100- 211 Genetics - Fall 2017 Bioinformatics Exercise for Investigation Disease-associated Genes and Alleles We will be using several publically-available databases on which to learn about our genes of interest. Most of them are a part of the National Center for Biotechnology Information (NCBI), which is funded by the National Institutes of Health (NIH). Others are held at private or public institutions. - provides information at the genetic level (gene structure, exon/intron, splice variants, tissue expression, location, etc) - Database of polymorphisms (including SNPs, indels, microsatellites, and non-polymorphic variants) that have clinical relavance. - Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB. - BLAST (Basic Local Alignment Search Tool) finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance. – CLUSTAL alignments. Tool used to show homology (relatedness) between proteins from different species. Does NOT show relatedness of species directly. - Online Mendelian Inheritance in Man. A great reference to start from if you want to learn about genes that are associated with diseases and disorders in human. For each of the questions, type answers in red font on this document. This finished document needs to be turned in to brightspace by WEDNESDAY 12/6/17 at midnight. We will start by investigating the NKX2-1 gene that is mutated in 40% of inherited thyroid cancers. NKX2-1 1. Go to and type in thyroid cancer. You will see a long list of genes that have been linked to thyroid cancer. Click the link for NKX2-1. The first paragraph usually has general information about the gene and associated protein. Use this paragraph and the rest of the page to answer the following questions. a. What are some other names for this gene? BCH;NK-2;TITF1;T/EBP;NMTC1 b. What type of protein does it encode? Thyroid-specific transcription factor c. What are some of the processes that your gene/protein are involved in?
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