• Author / Uploaded
• Friska Aprianti

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1.9. DNA NOTATION Imagine you have to write down a DNA sequence on a piece of paper. Which of these statements is true? I write the DNA sequence from 5’->3’ if it is the forward strand I write the DNA sequence from 3’->5’ if it is the reverse strand I write both strands of the DNA sequence, the forward as 5’->3’ and the reverse directly underneath as 3’->5’

Yes, you would write the sequence from 5’->3’ if it is the forward or the reverse strand. You may find 1.7 Grammatical rules for DNA sequence representation useful. Which is the reverse complement sequence of these 4 letter DNA string? ACTG GTCA TGAC CAGT

Remember that finding the reverse complement is a two step process. Correct! This is the reverse complement. This is a two step process. Let’s write the question sequence agains: ACTG The reverse sequence is GTCA and the complement of this is CAGT. You may find 1.8 Representing the reverse strand useful. 1.17.

For a given organism: Each amino acid is encoded by only one codon Each codon can encode only one amino acid Each amino acid is encoded by up to two different codons.

This is correct! You may find 1.10 From DNA to protein useful.

Select all statements that are true. Select all the answers you think are correct. the FASTA format is suitable for DNA and protein sequences the FASTA format is exclusive for DNA sequences the FASTA format is exclusive for protein sequences the FASTA format is suitable for RNA sequences

This is correct! Although not commonly used, RNA sequences can also be stored in FASTA format.

Select all statements that are true about a Genbank entry. Select all the answers you think are correct.

A Genbank entry has a section dedicated to sequence data. A typical Genbank entry has a section dedicated to sequence data in FASTA format. A Genbank entry includes the date of submission. A Genbank could or could not include a reference to published work.

2.7.

Which of these is NOT relevant for the process of homology annotation? Choose one option BLAST results protein 3D structure sequence accession number amino acid sequence conservation

An accession number or identifier is not related to protein function Which of these values given as results of a BLAST search will change if the size of the database is altered? percentage identity E-value score the percentage of coverage of a BLAST results depends on the query and the subject and do not depend on the size or nature of the database

the E-value depends, among other factors, on the size of the database You may find 2.4 Use of BLAST (Basic Local Alignment Search Tool) useful. In the BLAST submission page, which of the following can be used for entering the query sequence? Select all the answers you think are correct. paste a FASTA sequence upload a FASTA sequence file the protein name the protein accession number

TEST

1. You have downloaded this FASTA file but you are unable to use it for downstream analysis. By looking at the file, can you indicate why that is the case? NP_476772.1 alpha-Tubulin at 84B [Drosophila melanogaster] MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTVGGGDDSFNTFFSETGAGKHVPRAVFVDL EPTVVDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIVDLVLDRIRKLADQCTGLQGFLIFHS FGGGTGSGFTSLLMERLSVDYGKKSKLEFAIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIY DICRRNLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLVTYAPVISAEK AYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCMLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTG FKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE AREDLAALEKDYEEVGMDSGDGEGEGAEEY

the sequence is too small the sequence is a protein and FASTA files are only for nucleotides the “#” symbol is missing from the first line the “>” symbol is missing from the first line

CORRECT: The “>” symbol is needed to indicate the start of a FASTA sequence. It is the first character in the header of the sequence. You may find 1.16 EMBL, Genbank and FASTA file comparison - investigate and discuss useful.

Here is a short nucleotide sequence: ATCGTGATCG

which option represents the reverse complement sequence of the one shown above? GCTAGTGCTA CGATCACGAT TAGCACTAGC AUCGUGAUCG

CORRECT: This is the reverse complement You may find 1.7 Grammatical rules for DNA sequence representation useful. When comparing the GenBank and EMBL sequence data formats, the “COMMENT” field in the GenBank format corresponds to which field in the EMBL format? XX OC CC None of the above

CORRECT: CC corresponds to the Comment section You may find 1.13 The GenBank file format useful. One of your colleagues wants to investigate the beta-galactosidase enzyme in Clostridium difficile. Your colleague needs to retrieve the DNA sequence. They only have access to the protein sequence of a E. coli beta-galactosidase. You recommend them to:

Use the E. coli beta-galactosidase protein sequence to search Google. Type in “beta-galactosidase clostridium” in the search box in Uniprot Use the E. coli beta-galactosidase protein sequence as a query in BLASTp against nonredundant protein database Use the E. coli beta-galactosidase protein sequence as a query in tBLASTn against a defined database restricted to Clostridium species.

CORRECT: A tBLASTn search uses a protein query (which is the sequence that we have available) and searches a translated nucleotide database. Although the subject will be shown as an amino-acid sequence, the DNA sequence will be readily accessible from the BLAST results. You may find 2.3 BLAST, a tool for homology annotationuseful. When inspecting results from a BLASTp search the best match to a given query tends to be: The subject with the highest score The subject with the highest E-value The subject with similar length as the query All of the above You have used the entry for E. coli BamE protein from Uniprot as a resource and you need to add a citation. Which one is the most appropriate: www.uniprot.org The UniProt Consortium, UniProt: the universal protein knowledgebase, Nucleic Acids Res. 45: D158-D169 (2017) http://www.uniprot.org/uniprot/P0A937 You do not need to add a citation

CORRECT: This is a publication featuring the development and scope of Uniprot. What is more, this is Uniprot’s recommended citation.

You may find 2.13 A note on Versions and Citation useful.