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Preparing for EXAM II

Preparing for EXAM II - Known what types of information can...

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Known what types of information can be retrieved from different NCBI databases: Bookshelf (look up for a basic genetic concept, OMIM (online mendelian inheritance in man) Statistics – total = number of total genes in humans BLAST important tool for searching sequence databases Local alignment tool that displays the most strongly matching regions of the overall comparisons Structure ( 3D structure of protein) Pubmed ( literature) Protein (protein sequence of a gene) Nucleic acid, Conserved protein Domain Database (CDD)- resource for annotation of function units in proteins, collects domain models for set by NCBI and utilize 3D structure to provide insight into sequence, structure, and functional relationships Taxonomy- nomenclature of all organisms in public sequence databases (10% represented) UCSC Genome Browser MMDB- molecular model database, shows protein number and accession number Some terminology in bioinformatics RefSeq- accumulation of all genes compounded together, large RNA sequence collection EST- collection of short single-read transcript sequences, provide a resource for gene expression evaluating and potential varions E - value- comparing the similarities between two sequences, the lower the value the more significant the similarity between the two The lower the e-value the better the homology Score- calculated by sum of all the points of similarities and half similarities and differences together Query- sequence used to initiate the search Blastp- protein protein blast, blast against protein entry sequence database using a protein as a query. Blastn blast against a nucleotide sequence How to calculate % positive and % identity % identity ( count up all the letters under Query and divide by the total) % positive (count up the total (letters and +(similar but not identical) and divide by total In situ hybridization
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- use probe to hybridize RNA in fixed tissue, detects spatial information like which cells or which location mRNA expressed Synonymous- single nucleotide substitution does not change the amino acid by multiple codons, silent mutation ( sequencing and amino acid remain same) non-synonymous SNPs- does change amino acid with substitution Understand the difference between comparing two DNA sequences vs comparing two protein sequences Different types of DNA polymorphisms DNA polymorphism - one of two or more alternative forms of chromosomal locus that differ in nucleotide sequence or varying number of repeats Locus- specific point/region in the genome Alleles- genetic varients of polymorphic loci 4 categories most observed based on size, frequency within individual genomes and method used for detection - SNP single nucleotide polymorphism o Very frequent, 1 bp difference in ever 1000 alignment o Total difference in human genomes found 18 million SNPs o Single base-pair substitutions through chemicals or rare mistakes in replication o Useful as DNA markers, they are inherited, when comparing people’s genome sequence o Compare to other species by aligning the sequence and match up what is
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