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Bioinformatics Tutorial SBL1033

1) The student identified a DNA sequence 3222 base pairs in length using BLAST. 2) The sequence was found to likely be Entamoeba histolytica Gal/GalNAc lectin Igl2 mRNA. 3) The organism of origin was determined to be the protozoan Entamoeba histolytica.

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Nisha Lauren Vishvanath
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22 views

Bioinformatics Tutorial SBL1033

1) The student identified a DNA sequence 3222 base pairs in length using BLAST. 2) The sequence was found to likely be Entamoeba histolytica Gal/GalNAc lectin Igl2 mRNA. 3) The organism of origin was determined to be the protozoan Entamoeba histolytica.

Uploaded by

Nisha Lauren Vishvanath
Copyright
© © All Rights Reserved
Available Formats
Download as DOC, PDF, TXT or read online on Scribd
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Name : NANTHINI

Student ID : QUERY SEQUENCE 2

In short, you will copy one of the sequences from the data set, use nucleotide (blastn) in BLAST to
identify it, and use the information from your search to answer the question below. Instructions for
copying and pasting sequences are provided with the dataset. Instructions for using BLAST is
provided in your tutorial.

Materials:

 An internet connection
 Make a bookmark in your web browser to the NCBI website: http://www.ncbi.nih.gov
 A guide that shows how to do search and interpret the results is available at
ftp://ftp.ncbi.nlm.nih.gov/pub/factsheets/HowTo_BLASTGuide.pdf
 An overview on the BLAST interface is available on
http://blast.ncbi.nlm.nih.gov/about/#home
 A set of an "Query Sequences" (download in MyGuru) for you to identify.

Questions: Be sure to include the source of the information along with your answer. In this case, the
source will be the database or web page that provided the information.

1) How long is the sequence that was used to search the database?
Hint: This sequence is called "query" sequence because you used it to ask a question (or query)
of the database.
3222

2) What is the most likely identify of this sequence? What data supports this conclusion?
Hint: Refer to the slide in the BLAST tutorial that discuss the E-value.
Entamoeba histolytica Gal/GalNAc lectin Igl2 (igl2) mRNA

3) What organism was the most likely source of the sequence?


Hint: Refer to the BLAST tutorial to find an overview of the GenBank nucleotide record. If more
than one organism matches, look at the E- value to determine the most likely match.
Entamoeba histolytica HM-1:IMSS Gal/GalNAc lectin subunit Igl2,
mRNA
4) What is the common name for this organism?
Hint: Refer to the GenBank nucleotide record. It may also help to look at the Taxonomy
database. The BLAST tutorial shows where to find this link.

1 | B i o i n f o r m a ti c s T u t o r i a l S B L 1 0 3 3
Protozoa

5) What phylum contains this organism?


Hint: Refer to the taxonomy database. The BLAST tutorial shows how to find the link.
Eukaryotes

6) What is the accession number for the best-matching sequence?


AF337951

7) If possible, give the names of three different organisms with significant E-values. If organism
is represented, then write down the name of that organism.
Hint: Refer to the BLAST tutorial slide on E-value for description.
- Entamoeba histolytica HM-1:IMSS Gal/GalNAc lectin subunit
Igl2, mRNA
- Entamoeba histolytica beta 1 integrin-like protein mRNA, partial
cds

8) Use GenBank, PubMed, Gene, and UniGene records to find the possible function of the
protein that's specified by your DNA sequence. Describe what's known about the role of this
protein in the organism that provided the DNA.
- Carbohydrates bonding

2 | B i o i n f o r m a ti c s T u t o r i a l S B L 1 0 3 3

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