Pairwise ortholog matrix of cg.ezbiocloud.net
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This document provides instructions for exploring a pairwise ortholog matrix between genomes. It explains how to set the reference genome, ortholog detection method, and display options for the cells. Changing parameters requires clicking an apply button to update the table with the new settings.
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MYSTERY MOLECULE PROJECT, PART II(20 points total)BIO1001.docx
MYSTERY MOLECULE PROJECT, PART II
(20 points total)
BIO1001
Fall 2020
To complete the remainder of this project and prepare for your presentation, follow the instructions below. Your presentation should include the answers to all questions indicated below. For your final
presentation, you are expected to
organize your research and
present a rehearsed, 10-12
minute presentation using the rubric at the end of this document as a guideline for preparation.
Learning Objectives
At the conclusion of this phase of the mystery molecule project, students will be able to
1. Effectively navigate sequence databases of the NCBI website
a. BLAST DNA sequence against the human genome
b. Analyze alignment data from genomic
databases
c. Identify an unknown gene based on DNA sequence
2. Use
the scientific literature (primary and secondary resources)
to analyze gene products, and research the cellular and molecular basis of a disease gene.
3. Organize scientific content into a coherent presentation.
4. Communicate research results to a group of peers.
Step 1: BLAST your DNA sequence
1. Go to:
http://www.ncbi.nlm.nih.gov/
2. Click on BLAST (under “popular resources” at the right side of the screen)
3. Choose the nucleotide blast program (under “Web BLAST”)
4. In the “blastn” tab (on left) enter your DNA sequence into the “enter query sequence” box (obtain your mystery DNA sequences in the Mystery Molecule content area in D2L).
a. In “choose search set” click the “genomic + transcript databases”
b. From the drop down menu below, select “Human genomic + transcript (Human G + T)”
c. Under “program selection” in the next section down, optimize for highly similar sequences (megablast)
5. Submit query (click on “BLAST” at the bottom of the screen) and wait– this may take up to a few minutes.
6. A colorized map of sequence alignment scores will appear. Red indicates very good sequence alignment.
7. Scroll down to descriptions of sequences that produced statistically significant alignments. You should see options for genomic alignments and transcripts. An e-value close to zero, and maximum sequence identity close to 100% are optimal.
8. Identify your mystery gene/transcript from the description, e-value, and % sequence identity.
Step 2: Analysis of gene product
Click on the reference number (left, in the column labeled, “Accession”) for the mRNA transcript or genomic sequence of your mystery gene. Scroll down; you will see many references (titles, authors, years of publication) describing your gene. Clicking on any one of the PubMed reference numbers will link you directly to the original publication. You will need these publications to characterize your gene for your presentation. Bookmark this page—all your references must be from primary or secondary sources (no google, wikipedia, textbooks, blogs, etc.).
You must use a minimum of 7 references that can be found by searching NCBI.
OMIM.pptx
Online Mendelian Inheritance in Man (OMIM) is a continuously updated catalog of human genes and genetic disorders initiated in the 1960s. It provides unique six-digit identifiers for each entry and classifications for different types of entries. Searches can be performed using keywords, boolean operators, and gene/chromosome locations. However, OMIM does not contain a complete list of all entries and does not provide clinical evaluation or testing information.
Exercise 8, Human GeneticsActivity 1, Understanding genetics t.docx
Exercise 8, Human Genetics
Activity 1, Understanding genetics through chromosome analysis, #1-4
1. Figure 8-1 shows an example of a female karyotype.
Are there 46 total chromosomes? _____
How many pairs of autosomes are in the karyotype? _____
How many pairs of sex chromosomes? _____
2. Examine the homologous pair of sex chromosomes (Figure 8-1). Is there a visible difference between the maternal and paternal chromosomes? ______. Explain.
3. Figure 8-2 shows an example of a male karyotype.
Are there 46 total chromosomes? _____
How many pairs of autosomes are in the karyotype? _____
How many pairs of sex chromosomes? _____
4. Is there a visible difference between the X and Y chromosomes? _____ Explain.
Activity 2, Abnormal karyotypes, #1 and 3
1. In your report, include the following information:
Gender of patient: _________________
Description of any chromosomal abnormalities present in the karyotype: __________________
Name of abnormality (if present): ___________________
3. Would it be possible for the person who provided the karyotype in figure 8-5 to have a daughter with Down Syndrome if he or she had a spouse with a normal karyotype? Explain.
Activity 3, Relationship of chromosomes, genes, and alleles, #1-5
1. Which of the above genotypes represents an individual who is homozygous for the melanin trait? ______
2. Which of the genotypes listed in question one contains one maternal allele and one paternal allele? Explain.
3. Which genotype(s) listed in question one represent(s) an individual that is heterozygous? _____
4. Would there be a phenotypic difference between AA and Aa when the genes are expressed? Explain.
5. Which genotype listed in question one represents a person who is an albino? Explain.
Activity 4, Determining inheritance by combining alleles, #1-7
1. Based on your knowledge of dominant and recessive alleles, fill in the phenotypes for each allele combination.
Genotypes
Phenotypes
AA
Aa
aa
2. Combine the appropriate alleles to complete the other three boxes in the Punnett Square.
A
a
A
AA
a
What is the probability that this couple could have an albino child?
3. If this couple does have an albino child, what is the probability they could have a second albino child? Explain.
4. If this couple has a child with normal skin color, is there any possibility that this normal child could have an albino baby? Explain.
5. Is he correct in his assumption? Explain.
6. What are the genotypes of all the individuals mentioned in the problem?
Genotypes: Steve _____ Steve’s Mom _____ Steve’s Dad _____ Marilyn _____
7. What is the probability that Steve and Marilyn could have an albino child?
Probability of an albino child: _____
Probability of a child with normal skin color: _____
Exercise 9, Molecular Genetics
Activity 1, Building a DNA model, #1-8
1. Table 9-1, DNA Color Codes
Gummy Bear Color
DNA base
5. Your DNA model contains a total of _____ bases.
6. How many triplet ...
Comparative Genomics and Visualisation - Part 1
This document provides an overview of comparative genomics. It defines comparative genomics as combining genomic data and evolutionary biology to study genome structure, evolution and function. It discusses three levels of genome comparison: bulk properties like chromosome size and number, whole genome sequence similarity and organization, and functional genome features. The history of experimental comparative genomics is reviewed, noting that practical comparisons predated widespread genome sequencing.
Introduction to Apollo: A webinar for the i5K Research Community
This document provides an introduction and outline for a webinar on using the Apollo genome annotation editing tool. It was presented by Monica Munoz-Torres of BBOP to the i5K Research Community. The webinar aimed to help participants better understand genome curation in the context of automated and manual annotation. It also aimed to familiarize participants with Apollo's functionality and how to identify homologs of known genes, corroborate gene models using evidence, and modify automated annotations in Apollo. The document includes sections on genome sequencing projects, the objectives and uses of genome annotation, and a biological refresher on concepts relevant to manual annotation like genes, transcription, translation, and genome curation steps.
Essential Biology 4.3 Theoretical Genetics
The document provides a series of questions on genetics and heredity for students to answer. It includes questions about genotypes and phenotypes, Mendelian inheritance patterns such as dominant/recessive and codominant alleles, monohybrid and test crosses, pedigree charts, sex-linked traits and disorders like hemophilia and color blindness. Students are asked to complete tables, diagrams, calculations and explain concepts. Sources should be cited using CSE style and relevant terms highlighted before and after class.
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This document is a lab report for a biochemistry course that discusses DNA, RNA, and genetic information. The report summarizes databases that contain DNA and protein sequences, such as NCBI. It also discusses analyzing a DNA sequence to find an open reading frame and identify the encoded protein. Finally, the report discusses using BLAST to find homologous sequences and determine if sequences are homologous based on percent identity and E-values.
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The document describes a lab experiment analyzing gene expression data from human fibroblasts in response to serum using microarray analysis. The aims are to analyze the gene expression data using Excel and the ArrayTrack workbench. Key steps include importing microarray data into Excel and pre-treating the data by centering and scaling. ArrayTrack is then used to analyze the data through descriptive statistics, exploring gene expression profiles of gene lists, and using the significance analysis of microarrays (SAM) tool. Additional online databases like Gene Atlas and ArrayExpress are queried to find expression profiles and experimental data for a specific gene, APT13A2, under different conditions.
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You forgot to label some genome evolution data where you measured the number of
synonymous and nonsynonymous changes in the eeoB gene (a made up gene) in related insect
species that diverged roughly every 10 million years (My) over 200 My . Harn'e the data.
Complete the following statement so that it reads correctly: "Column A is the data. Column B is
the data and Column C is the data, obviously because the sites begin to around l'm so smart."
Hint: When you plot the data in your spreadsheet, put the time data (\#\# My) on the x-axis for
each of the other two data columns. Be prepared to share your plotted data and your answers, so
pick one person to plot the data and present it. MATERIALS -Microsoft Excel or Google Sheets
(or some kind of graphing software) You are a molecular geneticist attempting to understand fish
evolution. Specifically, you're looking at zebrafish (ZF) and common bream (CB) evolution
using ten genes (gene1-10) from their respective genomes. To accomplish this you will need to
perform a relative rates test, as described in class. As an outgroup for comparison, you will use
the dolphin. Below l've provided the info needed to perform a relative rates test. The cutoff for
significant differences is 1% . Here's the data: Using genome synteny plots to infer relatedness
between taxa The synteny plots below reflect both gene content and genomic structure (i.e.
location and orientation gene content) of three bacterial species: SoET, SoBr and SoEL. Use the
synteny data to identify which phylogeny (ignore branch lengths) below is accurate and correctly
complete the following passage: "Between SoBr and SoEL there are several -type
rearrangements, unlike between SoET and SoEL, which appears to have only of those kinds of
rearrangements. SoBr still shares many with SoEL. Based on the synteny plots, the phylogeny is
likely the most accurate and SoET and SoEL are more related to one another than either are to
SoBr ..
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After obtaining genetic variants from next generation sequencing data, a precursory step in tertiary analysis is to annotate each variant with available relevant information. There is no standardized compendium for this purpose; researchers instead are required to compile data from a motley of annotation tools and public datasets. These sources for annotation are independently maintained, and accordingly there is limited concordance between their reported contents. The choice of annotation datasets thus has a direct and significant impact on the results of the analysis.
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This document discusses genetic linkage and crossing over. It defines linkage as genes being inherited together on the same chromosome. Crossing over occurs during meiosis when segments are exchanged between non-sister chromatids, resulting in new combinations of linked genes. The frequency of crossing over between two genes increases with genetic distance. Three-point crosses allow determining gene order and calculating linkage distances between loci. Double crossovers are also discussed.
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Apollo is a web-based application that supports and enables collaborative genome curation in real time, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Apollo allows researchers to break down large amounts of data into manageable portions to mobilize groups of researchers with shared interests.
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Bioinformatica 08-12-2011-t8-go-hmm
The document outlines topics that will be covered in a bioinformatics course, including biological databases, sequence alignments, database searching, phylogenetics, protein structure, gene prediction, gene ontologies, hidden Markov models, and non-coding RNA. It then provides more details on topics like using sequence similarity to gather information from unknown protein sequences, finding conserved patterns in alignments using profiles and hidden Markov models, and challenges around gene prediction from raw genomic sequences.
MYSTERY MOLECULE PROJECT, PART II(20 points total)BIO1001.docx
MYSTERY MOLECULE PROJECT, PART II
(20 points total)
BIO1001
Fall 2020
To complete the remainder of this project and prepare for your presentation, follow the instructions below. Your presentation should include the answers to all questions indicated below. For your final
presentation, you are expected to
organize your research and
present a rehearsed, 10-12
minute presentation using the rubric at the end of this document as a guideline for preparation.
Learning Objectives
At the conclusion of this phase of the mystery molecule project, students will be able to
1. Effectively navigate sequence databases of the NCBI website
a. BLAST DNA sequence against the human genome
b. Analyze alignment data from genomic
databases
c. Identify an unknown gene based on DNA sequence
2. Use
the scientific literature (primary and secondary resources)
to analyze gene products, and research the cellular and molecular basis of a disease gene.
3. Organize scientific content into a coherent presentation.
4. Communicate research results to a group of peers.
Step 1: BLAST your DNA sequence
1. Go to:
http://www.ncbi.nlm.nih.gov/
2. Click on BLAST (under “popular resources” at the right side of the screen)
3. Choose the nucleotide blast program (under “Web BLAST”)
4. In the “blastn” tab (on left) enter your DNA sequence into the “enter query sequence” box (obtain your mystery DNA sequences in the Mystery Molecule content area in D2L).
a. In “choose search set” click the “genomic + transcript databases”
b. From the drop down menu below, select “Human genomic + transcript (Human G + T)”
c. Under “program selection” in the next section down, optimize for highly similar sequences (megablast)
5. Submit query (click on “BLAST” at the bottom of the screen) and wait– this may take up to a few minutes.
6. A colorized map of sequence alignment scores will appear. Red indicates very good sequence alignment.
7. Scroll down to descriptions of sequences that produced statistically significant alignments. You should see options for genomic alignments and transcripts. An e-value close to zero, and maximum sequence identity close to 100% are optimal.
8. Identify your mystery gene/transcript from the description, e-value, and % sequence identity.
Step 2: Analysis of gene product
Click on the reference number (left, in the column labeled, “Accession”) for the mRNA transcript or genomic sequence of your mystery gene. Scroll down; you will see many references (titles, authors, years of publication) describing your gene. Clicking on any one of the PubMed reference numbers will link you directly to the original publication. You will need these publications to characterize your gene for your presentation. Bookmark this page—all your references must be from primary or secondary sources (no google, wikipedia, textbooks, blogs, etc.).
You must use a minimum of 7 references that can be found by searching NCBI.
OMIM.pptx
Online Mendelian Inheritance in Man (OMIM) is a continuously updated catalog of human genes and genetic disorders initiated in the 1960s. It provides unique six-digit identifiers for each entry and classifications for different types of entries. Searches can be performed using keywords, boolean operators, and gene/chromosome locations. However, OMIM does not contain a complete list of all entries and does not provide clinical evaluation or testing information.
Exercise 8, Human GeneticsActivity 1, Understanding genetics t.docx
Exercise 8, Human Genetics
Activity 1, Understanding genetics through chromosome analysis, #1-4
1. Figure 8-1 shows an example of a female karyotype.
Are there 46 total chromosomes? _____
How many pairs of autosomes are in the karyotype? _____
How many pairs of sex chromosomes? _____
2. Examine the homologous pair of sex chromosomes (Figure 8-1). Is there a visible difference between the maternal and paternal chromosomes? ______. Explain.
3. Figure 8-2 shows an example of a male karyotype.
Are there 46 total chromosomes? _____
How many pairs of autosomes are in the karyotype? _____
How many pairs of sex chromosomes? _____
4. Is there a visible difference between the X and Y chromosomes? _____ Explain.
Activity 2, Abnormal karyotypes, #1 and 3
1. In your report, include the following information:
Gender of patient: _________________
Description of any chromosomal abnormalities present in the karyotype: __________________
Name of abnormality (if present): ___________________
3. Would it be possible for the person who provided the karyotype in figure 8-5 to have a daughter with Down Syndrome if he or she had a spouse with a normal karyotype? Explain.
Activity 3, Relationship of chromosomes, genes, and alleles, #1-5
1. Which of the above genotypes represents an individual who is homozygous for the melanin trait? ______
2. Which of the genotypes listed in question one contains one maternal allele and one paternal allele? Explain.
3. Which genotype(s) listed in question one represent(s) an individual that is heterozygous? _____
4. Would there be a phenotypic difference between AA and Aa when the genes are expressed? Explain.
5. Which genotype listed in question one represents a person who is an albino? Explain.
Activity 4, Determining inheritance by combining alleles, #1-7
1. Based on your knowledge of dominant and recessive alleles, fill in the phenotypes for each allele combination.
Genotypes
Phenotypes
AA
Aa
aa
2. Combine the appropriate alleles to complete the other three boxes in the Punnett Square.
A
a
A
AA
a
What is the probability that this couple could have an albino child?
3. If this couple does have an albino child, what is the probability they could have a second albino child? Explain.
4. If this couple has a child with normal skin color, is there any possibility that this normal child could have an albino baby? Explain.
5. Is he correct in his assumption? Explain.
6. What are the genotypes of all the individuals mentioned in the problem?
Genotypes: Steve _____ Steve’s Mom _____ Steve’s Dad _____ Marilyn _____
7. What is the probability that Steve and Marilyn could have an albino child?
Probability of an albino child: _____
Probability of a child with normal skin color: _____
Exercise 9, Molecular Genetics
Activity 1, Building a DNA model, #1-8
1. Table 9-1, DNA Color Codes
Gummy Bear Color
DNA base
5. Your DNA model contains a total of _____ bases.
6. How many triplet ...
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The document discusses Mendelian genetics concepts including:
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Drug Tanzeum
Diseases Diabetes
Gene and Gene Product glucagon-like peptide (GLP)-1 fusion protein
Gene ID GCG
Structure 3IOL
1. Report on Gene and Related Protein (3-4 pages) (30 pts) (details on navigation of PubMed site in separate Power Point)
a. The name and gene code for your gene product/protein.
b. Determine chromosome location of your gene. Paste a picture of the chromosome from MAP VIEWER into your report and describe.
c. Identify the size of the coding region of your gene, include a link to the GENE page, and explain what the coding region is. Note: your gene sequence may be very long, do not cut and paste the sequence into your report.
d. Determine the intron /exon structure of your gene including the number of introns and exons. Cut and paste a schematic diagram of your gene into the report, indicate position of introns, and exons, and provide a caption for the figure that describes how the sequence of the primary mRNA transcript is related to the gene (DNA) sequence.
e. Identify the sequence of the mature mRNA and copy this sequence into your report with the appropriate link to this sequence. (Note: the mRNA sequence will actually be shown as a “complementary DNA” or “cDNA.” The sequence given in the database is an exact copy of the mRNA sequence, except that it has T instead of U. ) Explain how this sequence is derived from the sequence of the coding region identified above.
f. Identify the Open reading frame in the mature mRNA (Coding sequence, CDS) Find the START codon, STOP codon, and highlight the open reading frame. Explain where translation begins and ends.
g. Translate the first ten amino acids of the Open Reading Frame.
h. Identify the protein sequence, and copy this sequence into your report with a link to the appropriate page. Check the first ten amino acids of the database protein sequence against the ten amino acids you translated above.
i. Compare your (human) gene sequence with the same gene sequence from other species. Copy a representative portion of the sequence alignment into your report that shows the similarities/differences between the human protein sequence and the homologous protein sequence from at least one other species. (Note: sequences will align if you use the Courier font). Explain how the similarity/difference in sequences explains the similarities and differences between species.
j. Paste a picture of the secondary (worm view) and tertiary (space filling) structures of your protein into your report. Note: structures have not been determined for all proteins, so you may have been given an identifier for a similar protein. Describe things about the structure, for example features of the shape, charge, or hydrophobicity.
Genome database assignment and stepwise instructions
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The exercise:
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- 2. B I O I N F O R M A T I C S M A D E E A S Y / C h u n L a b , I n c . 2 Set the “Reference genome” here. Orthologs are displayed in the direction of Reference → Subject genome. In this case, Reference genome is the second column. Set the “Data Type” or algorithm for ortholog detection. RBH (Reciprocal Best Hit) is protein-based whereas ORF-independent is DNA-based. How to explore pairwise ortholog matrix 1 2 1 2
- 3. B I O I N F O R M A T I C S M A D E E A S Y / C h u n L a b , I n c . 3 Set the display option in cells. “Contig# begin” displays the index (starting from 1) of contigs of the genome and their begin-positions. “Bit score ratio (%)” displays how similar the sequences are between “Reference” and “Subject” genomes. 3 3 How to explore pairwise ortholog matrix
- 4. B I O I N F O R M A T I C S M A D E E A S Y / C h u n L a b , I n c . 4 Set the display option in cells. “Contig# begin” displays the index (starting from 1) of contigs of the genome and their begin-positions. “Bit score ratio (%)” displays how similar the sequences are between “Reference” and “Subject” genomes. Click [Apply] button for applying parameters. The content of table will remain unchanged until this button is clicked. 3 4 3 4 How to explore pairwise ortholog matrix