Assignment 7 – DNA Modeling
Dean ZellerDue: Thursday, November 8th
CS1005110 points
Fall, 2007
Objective The student will create a structurally accurate model of an actual DNA strand out of pipe cleaners, and an accompanying report on the strand.
Website:
ncbi:National Center for Biotechnology Information
nlm:National Library of Medicine
nih:National Institutes of Health
Readings
Activity 7
Background: CoreNucleotide (DNA Sequence Database)
The National Center for Biotechnology Information maintains a web page of discovered DNA sequences in organisms. There is an intense amount of work by scientists to create these databases. We will use this database to find actual sequences of DNA to model.
Instructions
Follow these steps to create a DNA model:
1)Go to the NCBI website and select a DNA sequence to model.
- Go to the NCBI website.
- In the search text-box, enter the name of an organism, and click Go.
- Click the CoreNucleotide database.
- Find a DNA sequence that suits your needs. Check the source organism; your search term may be somewhere else in the report.
2)Create a report on your strand, following the template. Use copy and paste for report material. The report should be one page (two if necessary).
3)Create a model of a section of the DNA strand in the report. Choose a starting position in the DNA sequence, and work from there. You need not start at the beginning.
4)When complete with the model, boldface and outline the section included in the model and any other relevant information in the report.
Turning in your assignment
- Make a printout of your report.
- Turn in the model and the report.
Grading
You will be graded on the following criteria:
AccuracyCorrect representation of base pairs in the model
ReadabilityQuality of the report (complete, concise)
EffortQuantity, length, and quality of model created
Extra Credit
- Length of model – 200 base pairs
DNA Modeling Report
Dean Zeller
CS10051
Search parameter: earthworm
Source:National Center for Biotechnology Information (
Model:Base Pairs 101 through 200
Report
LOCUS EU155485 342 bp mRNA linear INV 08-OCT-2007
DEFINITION Lumbricus terrestris gelsolin-related protein EWAM mRNA, partial
cds.
ACCESSION EU155485
VERSION EU155485.1 GI:157824625
KEYWORDS .
SOURCE Lumbricus terrestris(common earthworm)
ORGANISM Lumbricus terrestris
Eukaryota; Metazoa; Annelida; Clitellata; Oligochaeta; Haplotaxida;
Lumbricina; Lumbricidae; Lumbricus.
REFERENCE 1 (bases 1 to 342)
AUTHORS Krueger,E.M.I., Hinssen,H. and D'Haese,J.
TITLE A gelsolin-related protein involved in spermatogenesis of the
earthworm Lumbricus terrestris
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 342)
AUTHORS Krueger,E.M.I. and D'Haese,J.
TITLE Direct Submission
JOURNAL Submitted (14-SEP-2007) Institut fuer Zoomorphologie, Zellbiologie
und Parasitologie, Heinrich-Heine Universitaet Duesseldorf,
Universitaetsstr. 1, Duesseldorf 40225, Germany
FEATURES Location/Qualifiers
source 1..342
/organism="Lumbricus terrestris"
/mol_type="mRNA"
/db_xref="taxon:6398"
/sex="male"
/cell_type="germ cells"
/tissue_type="seminal vesicle"
CDS <1..>342
/note="similar to gelsolin-related protein EWAM isoform P1
from muscle in GenBank Accession Number D29920"
/codon_start=1
/product="gelsolin-related protein EWAM"
/protein_id="ABV82435.1"
/db_xref="GI:157824626"
/translation="VNFKVTEWPQNQHGKFYNGDSYIILNTYKPDPKSNELAYDVHFW
IGSQSSQDEYGTAAYKTVELDTFLDDKPVQHREVQGYESELFRNYFKQGLTILEGGAE
TGFHHVKPTEYK"
ORIGIN
1 gtgaatttca aggtgactga atggccacag aaccaacacg gaaagttcta caacggagat
61 tcctacatca ttctaaacac gtacaagccg gacccgaaga gcaatgaact ggcctatgac
121 gttcacttct ggattggcag tcaaagttcc caggatgagt atggaacggc tgcgtacaag
181 acggtggagc tggatacgtt ccttgacgac aaaccagttc aacatcgcga ggtccaaggt
241 tacgagtcgg aactcttccg aaactacttc aagcaaggac tgacgatcct tgagggtgga
301 gctgagactg gattccacca cgtgaaacca acggaataca aa