Escuela Superior Politécnica del Litoral

Integrantes: Limones Gabriel, Moreira Kevin, Peralta Jean

Part 1: Identify sequences with Blast

First Sequence

1. In the Descriptions section, look at the top result, which should be the result with
the highest score. Write down information about the best match:

 Description (no need to write the whole thing): Homo sapiens CF

transmembrane conductance regulator (CFTR), RefSeqGene (LRG_663)
on chromosome 7
 E value: 0.0
 Identity: 503/503
 Query cover: 100%

2. Now scroll down to the Alignments heading. Look at the top result, which should
be the same one. Look at the alignment between your query and the reference.
Do you see any mismatches? There aren’t gaps and there aren’t mismatches.
3. How can you judge whether this is a good match? We don’t realize that our
identity percentage is 100%. In addition, we see that there aren’t gaps between
the 503 nucleotides that we are looking for in the sequence.
4. What is this gene? Google the name of the gene and write down something
significant you learned about it.

This gene encodes a member of the ATP-binding cassette (ABC) transporter

superfamily. The encoded protein functions as a chloride channel, making it unique
among members of this protein family, and controls ion and water secretion and
absorption in epithelial tissues.
 Second sequence

1. In the Descriptions section, look at the top result, which should be the result with
the highest score. Write down information about the best match:

 Description (no need to write the whole thing): Homo sapiens CF

transmembrane conductance regulator (CFTR), RefSeqGene (LRG_663)
on chromosome 7
 E value: 0.0
 Identity: 500/503
 Query cover: 100%
2. Now scroll down to the Alignments heading. Look at the top result, which should
be the same one. Look at the alignment between your query and the reference.
Do you see any mismatches? In query 241 to 297 there is 3 gaps of 503 nucleotids,
and identity about 500 of 503 so there is no mismatches.
3. How can you judge whether this is a good match? You can see it identity, Gap and
E value is good. If you relate gap and identity you can see if sequence have a
mismatch so if mismatches are high, it can’t be a good match and also Evalue( near
to 0.0 is good, near to 1 is bad)
4. What is this gene? Google the name of the gene and write down something
significant you learned about it.

According to ncbi nih, this gene controls ion and water secretion and absorption in
epithelial tissues
Part 2: Investigating sets of sequences

Each of the following sets of sequences was obtained from a sequencing experiment.

For each experiment, answer these questions:

- Set 1
1. What do these sequences have in common?

These 3 nucleotide sequences belong to vertebrate animals, Bos taurus, Sus scrofa
domesticus and Cephalophorus cf. kivuensis, respectively. In these sequences we
observe that they do not have gaps or mismatches. Regarding their taxonomy, they are
even-toed ungulate organisms

2. What is your best guess about the original purpose of this experiment?

They are taking samples, either partial or complete, from three animals of different
species, but which share specific characteristics such as having even-toed ungulates
known as artiodactyls. Likewise, these animals have a stomach divided into four parts,
they have a mobile lower jaw that allows them to chew, among other things.

- Set 2

1. What do these sequences have in common?

The tree sequences have a 60-nucleotide length, they didn’t have any gaps nor
mismatch, similar E-value and percent identity. The only similarity that they have is
that all nucleotide sequences are from macroorganisms.

2. What is your best guess about the original purpose of this experiment?

According to literature, the first sequence is from Arabidopsis thaliana, a model plant
species, ideal for genetic sequences related to understanding gene functions from
many plants. Then, we have Hexokinase 1 and 1-like, basically an enzyme group who
actively participates in glycolysis. It makes me think that A. thaliana chromosome 4 is
responsible for glycolysis. I can think in 2 options: first, is a comparison of how plants
metabolize glucose against animals, so that’s why took a genome base plant
comparing to another plant (only as prediction) and a common tester animal species as
Mus musculus is (predicted genome too). Second, could be how is metabolization of
glucose pathway from Malus domestica to Mus musculus, what genes are expressed
and what genes aren’t. in summary, a comparison of two different kingdom species
who have the same function to produce glucose from sources, using a base genetic
model (A. thaliana), to predict the possible nucleotide sequence in each species.

- Set 3

1. What do these sequences have in common?

Of the 3 sequences that we found in set 3, we noticed that they were Gram-positive
Trueperella pyogenes bacteria and an uncultivated Grand negative bacterial clone,
specifically partial sequences of the 16S ribosomal RNA gene. Likewise, the sequences
do not present gaps, however they do present mismatches.

2. What is your best guess about the original purpose of this experiment?

The study of bacteria is fundamental because it helps us to develop effective

treatments and vaccines for the diseases caused by it.