Bioinformatics

PRACTICAL EXERCISE 1

This exercise will focus on DNA and protein alignment tools available and further information
linked to databases on the web. Please write answers on the Answer sheet.

(a) Global access to NCBI databases

Bioinformatics databases may be queried via

GQuery, the NCBI Global Cross-database Search accessed at:
http://www.ncbi.nlm.nih.gov/gquery/

You can query by keywords, accession number, sequence fragment etc. The nucleotide
sequence database query (GenBank, EMBL and DDBJ) is available at
http://www.ncbi.nlm.nih.gov/nuccore/

Using the cross-database interface you can see sequence annotation, published links
accessible via links to PubMed (at NCBI), and links to related sequences (neighbours).

PubMed is accessible directly at http://www.ncbi.nlm.nih.gov/pubmed for direct keyword or

author queries.

In addition to GenBank, the search engine allows you to search a range of other databases,
including whole genome sequences, single nucleotide polymorphisms (SNPs), population-
based datasets, functional and structural information on gene products, and taxonomic
information.

Explore some of these databases by clicking on the icons on the GQuery front page.
Three examples:
 Genome > enter Pan troglodytes in the search box
How many chromosomes? What is its lineage? Complete on answer sheet (at end).

 Homologene > search for Pax6 and find its homologues in human, cow, chicken, fruit
fly etc.
Write the Gene ID for each on the answer sheet.

 PubChem Compound> search the common antibiotic amoxicillin and determine its
Mechanism of Action under biomedical interaction and pathway
Write on answer sheet

(b) Extraction of DNA and protein sequences from GenBank

Sequences can be accessed by searching for an organism, gene, author name or key word.

Go to http://www.ncbi.nlm.nih.gov/gquery/ and choose the nucleotide database.

Query for the E00389 DNA sequence in the Nucleotide menu, and then choose to see it in
FASTA format from the display formats menu option. The sequence may be extracted via "cut
and paste”.

Search in the Nucleotides menu option, for the key words orotidine and decarboxylase. This
will give a list of matching sequences. Note the large number. This enzyme is found in many

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organisms. View the Tree (right side of page) with organisms in which this enzyme has been
identified.
Write the names of five animals for which the enzyme sequence is available, on your answer
sheet.

Globsters and Monsters of the Deep

For hundreds of years there has been a

belief that the depth of the ocean
contains sea monsters. This was
supported by ‘observations’ with
drawing and paintings and with hard
evidence of pieces of the ‘sea
monsters’ found on beaches. This scifi
like mystery has remained for centuries until the last decade with the development of DNA
sequencing and DNA alignment databases. A sample was analysed of the infamous “Chilean
blob”. See for yourself the analysis.

Now type “Chilean blob” into the GQuery search across databases. You should see the number
three listed next to the Nucleotide Icon on the GQuery front page. If you click on this icon you
retrieve three sequences from an unusual case study you may have heard of. Note their
accession numbers: AY582746, AY582747, AY582748. Each GenBank submission is assigned a
unique accession (identification) number that can be used to retrieve that sequence from the
database.

Type AY582746 into GQuery. You should retrieve the same sequence.

 On the Answer sheet provide the title of the reference associated with the sequence.

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Answers:
a) Pan troglodytes
Chromosomes: 23
Lineage:
Eukaryota[3392]; Metazoa[1117]; Chordata[547]; Craniata[537]; Vertebrata[537]; Eut
eleostomi[528]; Mammalia[185]; Eutheria[179]; Euarchontoglires[76]; Primates[33];
Haplorrhini[26]; Catarrhini[21]; Hominidae[6]; Pan[2]; Pan troglodytes[1]

Pax 6
Human (Homo sapiens): 5080
Chimpanzee (Pan troglodytes): 737387
Cattle (Bos Taurus): 286857
Chicken (Gallus gallus): 395943
Fruitfly (Drosophila melanogaster): 43833

Amoxicillin
Mechanism of Action: Amoxicillin binds to penicillin-binding protein 1A (PBP-1A)
located inside the bacterial cell well. Penicillins acylate the penicillin-sensitive
transpeptidase C-terminal domain by opening the lactam ring. This inactivation of the
enzyme prevents the formation of a cross-link of two linear peptidoglycanstrands,
inhibiting the third and last stage of bacterial cell wall synthesis. Cell lysis is then
mediated by bacterial cell wall autolytic enzymes such as autolysins; it is possible that
amoxicllin interferes with an autolysin inhibitor.

b) E00389
E00389.1 DNA coding for cellobiohydrolase I
AAGGTTAGCCAAGAACAATAGCCGATAAAGATAGCCTCATTAAACGGAATGAGCTAGTAGGCAAAGTCAGCGAATGT
GTATATATAAAGGTTCGAGGTCCGTGCCTCCCTCATGCTCTCCCCATCTACTCATCAACTCAGATCCTCCAGGAGACTTG
TACACCATCTTTTGAGGCACAGAAACCCAATAGTCAACCGCGGACTGGCATCATGTATCGGAAGTTGGCCGTCATCAC
GGCCTTCTTGGCCACAGCTCGTGCTCAGTCGGCCTGCACTCTCCAATCGGAGACTCACCCGCCTCTGACATGGCAGA
AATGCTCGTCTGGTGGCACTTGCACTCAACAGACAGGCTCCGTGGTCATCGACGCCAACTGGCGCTGGACTCACGCT
ACGAACAGCAGCACGAACTGCTACGATGGCAACACTTGGAGCTCGACCCTATGTCCTGACAACGAGACCTGCGCGA
AGAACTGCTGTCTGGACGGTGCCGCCTACGCGTCCACGTACGGAGTTACCACGAGCGGTAACAGCCTCTCCATTGGC
TTTGTCACCCAGTCTGCGCAGAAGAACGTTGGCGCTCGCCTTTACCTTATGGCGAGCGACACGACCTACCAGGAATT
CACCCTGCTTGGCAACGAGTTCTCTTTCGATGTTGATGTTTCGCAGCTGCCGTAAGTGACTTACCATGAACCCCTGAC
GTATCTTCTTGTGGGCTCCCAGCTGACTGGCCAATTTAAGGTGCGGCTTGAACGGAGCTCTCTACTTCGTGTCCATGG
ACGCGGATGGTGGCGTGAGCAAGTATCCCACCAACAACGCTGGCGCCAAGTACGGCACGGGGTACTGTGACAGCCA
GTGTCCCCGCGATCTGAAGTTCATCAATGGCCAGGCCAACGTTGAGGGCTGGGAGCCGTCATCCAACAACGCAAAC
ACGGGCATTGGAGGACACGGAAGCTGCTGCTCTGAGATGGATATCTGGGAGGCCAACTCCATCTCCGAGGCTCTTAC
CCCCCACCCTTGCACGACTGTCGGCCAGGAGATCTGCGAGGGTGATGGGTGCGGCGGAACTTACTCCGATAACAGAT
ATGGCGGCACTTGCGATCCCGATGGCTGCGACTGGAACCCATACCGCCTGGGCAACACCAGCTTCTACGGCCCTGGC
TCAAGCTTTACCCTCGATACCACCAAGAAATTGACCGTTGTCACCCAGTTCGAGACGTCGGGTGCCATCAACCGATAC
TATGTCCAGAATGGCGTCACTTTCCAGCAGCCCAACGCCGAGCTTGGTAGTTACTCTGGCAACGAGCTCAACGATGAT
TACTGCACAGCTGAGGAGACAGAATTCGGCGGATCTCTTTCTCAGACAAGGGCGGCCTGACTCAGTTCAAGAAGGC
TACCTCTGGCGGCATGGTTCTGGTCATGAGTCTGTGGGATGATGTGAGTTTGATGGACAAACATGCGCGTTGACAAA
GAGTCAAGCAGCTGACTGAGATGTTACAGTACTACGCCAACATGCTGTGGCTGGACTCCACCTACCCGACAAACGAG
ACCTCCTCCACACCCGGTGCCGTGCGCGGAAGCTGCTCCACCAGCTCCGGTGTCCCTGCTCAGGTCGAATCTCAGTC
TCCCAACGCCAAGGTCACCTTCTCCAACATCAAGTTCGGACCCATTGGCAGCACCGGCAACCCTAGCGGCGGCAACC
CTCCCGGCGGAAACCGTGGCACCACCACCACCCGCCGCCCAGCCACTACCACTGGAAGCTCTCCCGGACCTACCCAG
TCTCACTACGGCCAGTGCGGCGGTATTGGCTACAGCGGCCCCACGGTCTGCGCCAGCGGCACAACTTGCCAGGTCCT
GAACCCTTACTACTCTCAGTGCCTGTAAAGCTCCGTGCGAAAGCCTGACGCACCGGTAGATTCTTGGTGAGCCCGTAT
CATGACGGCGGCGGGAGCTACATGGCCCCGGGTGATTTATTTTTTTTGTATCTACTTCTGACCCTTTTCAAATATACGG
TCAACTCATCTTTCACTGGAGATGCGGCCTGCTTGGTATTGCGATGTTGTCAGCTTGGCAAATTGTGGCTTTCGAAAA
CACAAAACGATTCCTTAGTAGCCATGCATTTTAAGATAACGGAATAGAAGAAAGAGGAAATTAAAAAAAAAAAAAAA
ACAAACATCCCGTTCATAACCCGTAGAATCGCCGCTCTTCGTGTATCCCAGTACCA

Orotidine and Decarboxylase

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1. Fundulus Heteroclitus (mummichog)
2. Lygus Hesperus (lygus bug)
3. Mus Musculus (house mouse)
4. Dorsophila Melanogaster (fruit fly)
5. Macaca Mulatta (Rhesus monkey)

Chilean Blob
AY582746
Title: Microscopic, biochemical, and molecular characteristics of the Chilean Blob and
a comparison with the remains of other sea monsters: nothing but whales