Question

x Assignment 1 - Database.pdf ... Learn how to access and use NCBI databases Question 1: Search Taxonomy database for: 1) Homo sapiens, 2) Heterodoxus macropus, 3) E. coli. a. What is the common name of the species? b. How many nucleotide or protein sequence records do you find (show your search results in cropped windows)? Question 2: Use the name "plague thrips" to search the Nucleotide database. a. What is the scientific name of the plague thrips? b. How many sequence records do you find? c. Which genes or genomes of the plague thrips have been sequenced? d. Provide information of the most recent publication that reported the mitochondrial genome of the plague thrips including the authors, year and title of the publication, title of the journal, volume and page numbers. Question 3: Search PubMed for "Thanh NM" (International University). a. How many publications of Thanh NM were deposited in PubMed? b. List the common names of 2 aquatic animals that Thanh NM worked on. c. Provide information of publication by Thanh NM: year and title of the publication, title of the journal, volume and page numbers. Question 4: Search Genome database for Homo sapiens. a. How many records did your search find? b. Provide the GenBank accession number for the chromosome 1 of Homo sapiens, the size of the chromosome 1. c. Provide information of the most recent publication that reported the chromosome 1 including the authors, year and title of the publication, title of the journal, volume and page numbers. Question 5: Use accession number "CU329670" to search the Nucleotide database. a. What is the type of sequence? What is the length of sequence? What is the name of database division? b. What is the scientific name of organism? Go to the FEATURES section of the record. Link to the CDS to gain access to the first 5662 nucleotides of the sequence. c. Name the protein product of the CDS and the length of protein. d. Write the first four amino acids. e. Write the nucleotide sequence of the coding strand that corresponds to these amino acids. f. Write the nucleotide sequence of the template strand that corresponds to these amino acids (Note that the definition of the coding strand is the strand of DNA within the gene that is identical to the transcript and the template strand is the strand that is complementary to the coding strand.)

Answer 1

Answer 1:

a. Common name of Homo sapiens is Human, Heterodoxus macropus is Wallaby louse, and E.coli is E.coli or gram negative rod shape bacteria.

b. Homo sapiens: Nucleotide records - 27613709, Protein records - 1380761

Heterodoxus macropus: Nucleotide records - 2, Protein records - 26

  E.coli: Nucleotide records - 7749435, Protein records - 57185393
f = c n cbi.nlm.nih.gov/protein?term=txid9606[Organism] NCBI Resources How To Sign in to NCBI Protein Protein Search txid9606[Organism]|| Create alert Advanced Help COVID-19 is an emerging, rapidly evolving situation. Get the latest public health information from CDC: https://www.coronavirus.gov. Get the latest research from NIH: https://www.nih.gov/coronavirus. Get the latest Summary - 20 per page - Sort by Default order Send to: Filters: Manage Filters Species Animals (1,380,748) Fungi (7) Bacteria (2) Viruses (2) Customize See the results of this search (1220840 items) in our new Identical Protein Groups database. Results by taxon Top Organisms Treel Homo sapiens (1380760) Danio rerio (1) Items: 1 to 20 of 1380761 << First < Prev Page 1 of 69039 Next > Last >> Source databases PDB (108,058) RefSeq (113,568) UniProtKB / Swiss- Prot (20,452) Customize ... Find related data Database: Select MHC class I antigen, partial [Homo sapiens] 273 aa protein Accession: BCB28916.1 GI: 1820736260 GenPept identical Proteins FASTA Graphics Find items Genetic compartments Mitochondrion (671,816) Plasmid (77) Plastid (3) MHC class I antigen, partial [Homo sapiens] 273 aa protein Accession: BCB28915.1 GI: 1820736258 GenPept Identical Proteins FASTA Graphics Search details txid9606[Organism] Sequence length Custom range... Molecular weight MHC class I antigen, partial [Homo sapiens) 365 aa protein 3.

3 NCBI Resources How To Sign in to NCBI Nucleotide Nucleotide Search txid9606fOrganism Create alert Advanced Help COVID-19 is an emerging, rapidly evolving situation. Get the latest public health information from CDC: https://www.coronavirus.gov. Get the latest research from NIH: https://www.nih.gov/coronavirus. Get the latest Summary - 200 per page - Sort by Default order Send to: Filters: Manage Filters Species Animals (27,556,432) Viruses (4,545) Customize ... Items: 1 to 200 of 27613709 Last >> Molecule types genomic DNA/RNA (15,212,524) mRNA (9,796,790) rRNA (46) Customize ... << First < Prev Page 1 of 138069 Next > Homo sapiens HLA-A gene for MHC class I antigen, partial cds, allele: HLA-A*66:05 1,022 bp linear DNA Accession: LC533107.1 GI: 1820736259 GenBank FASTA Graphics Results by taxon Top Organisms Treel Homo sapiens (27555199) synthetic construct (57258) Mus musculus (1080) Human papillomavirus type 16 (78) Trypanosoma cruzi (21) All other taxa (73) More... Source databases INSDC (GenBank) (27,271,810) RefSeq (187,027) Customize ... Homo sapiens HLA-C gene for MHC class I antigen, partial cds, allele: HLA-C*12:44 1,022 bp linear DNA Accession: LC533106.1 GI: 1820736257 GenBank FASTA Graphics Find related data Database: Select Find items Sequence Type Nucleotide (17,125,087) EST (8,705, 110) GSS (1,783,512) O 3. Homo sapiens HLA-C gene for MHC class I antigen, partial cds, allele: HLA-C*JRC-C-021 1,696 bp linear DNA Accession: LC533105.1 GI: 1820736255 GenBank FASTA Graphics Genetic compartments Search details txid96061 Organism

f c n cbi.nlm.nih.gov/nucleotide?term=txid145266[Organism] NCBI Resources How To Sign in to NCBI Nucleotide Nucleotide Search txid 145266 Organism] Create alert Advanced Help COVID-19 is an emerging, rapidly evolving situation. Get the latest public health information from CDC: https://www.coronavirus.gov. Get the latest research from NIH: https://www.nih.gov/coronavirus. Summary - Sort by Default order Send to: Filters: Manage Filters Species Animals (2) Customize Items: 2 Analyze these sequences Run BLAST Molecule types genomic DNA/RNA (2) Customize ... Source databases INSDC (GenBank) (1) RefSeq (1) Customize ... Heterodoxus macropus mitochondrion, complete genome 14,670 bp circular DNA Accession: AF270939.1 GI: 12328587 Protein PubMed Taxonomy GenBank FASTA Graphics Find related data Database: Select Find items Sequence Type Nucleotide (2) Heterodoxus macropus mitochondrion, complete genome 14,670 bp circular DNA Accession: NC_002651.1 GI; 12383036. BioProject Protein PubMed Taxonomy GenBank FASTA Graphics Genetic compartments Mitochondrion (2) Search details txid145266[Organism] Sequence length Custom range... Release date https://www.ncbi.nlm.nih.gov/nuccore/AF270939.1 Search See more...

f = c n cbi.nlm.nih.gov/protein 3 NCBI Resources How To Sign in to NCBI Protein Protein Search txid145266[Organism] Create alert Advanced Help COVID-19 is an emerging, rapidly evolving situation. Get the latest public health information from CDC: https://www.coronavirus.gov. Get the latest research from NIH: https://www.nih.gov/coronavirus. Get the lates Summary - 50 per page - Sort by Default order Send to: Filters: Manage Filters Species Animals (26) Customize See the results of this search (13 items) in our new Identical Protein Groups database. Find related data Database: Select Source databases Refeq (13) Customize ... Items: 26 Find items Genetic compartments Mitochondrion (26) ATP synthase 8 (mitochondrion) [Heterodoxus macropus] 53 aa protein Accession: AAG526571 Gl: 12328600 Nucleotide PubMed Taxonomy GenPept identical Proteins FASTA Graphics Search details txid145266[Organism] Sequence length Custom range... Molecular weight Custom range... Release date Custom range... ATP synthase 6 (mitochondrion) [Heterodoxus macropus] 218 aa protein Accession: AAG52656.1 GI: 12328599 Nucleotide PubMed Taxonomy GenPept identical Proteins FASTA Graphics Search See more... Revision date Custom range. Recent activity cytochrome oxidase subunit II (mitochondrion [Heterodoxus macropus] https://www.nih.gov/coronavirus Turn Off Clear

f = c n cbi.nlm.nih.gov/nucleotide NCBI Resources How To Sign in to NCBI Nucleotide Nucleotide Search txid562[Organism Create alert Advanced Help COVID-19 is an emerging, rapidly evolving situation. Get the latest public health information from CDC: https://www.coronavirus.gov. Get the latest research from NIH: https://www.nih.gov/coronavirus. Summary - 200 per page - Sort by Default order Send to: Filters: Manage Filters Species Animals (3) Plants (4) Fungi (6) Bacteria (7,749,332) Viruses (23) Customize ... Items: 1 to 200 of 7749435 << First <Prev Page 1 of 38748 Next > Last >> Results by taxon Top Organisms Tree Escherichia coli (7749304) synthetic construct (38) Fusarium graminearum (6) Mus musculus (3) Escherichia phage Mu (3) All other taxa (81) O Escherichia coli strain 643226, whole genome shotgun sequencing project 1. 314 rc linear DNA This entry is the master record for a whole genome shotgun sequencing project and contains no sequence data. Accession: AAAFTK000000000.2 GI: 1820560512 Assembly. GenBank Molecule types genomic DNA/RNA (7,746,041) mRNA (175) rRNA (28) Customize More... Source databases INSDC (GenBank) (4,273,805) RefSeq (3,470,629) Customize ... Find related data Database: Select O Find items Sequence Type Nucleotide (7,748,706) GSS (729) Escherichia coli strain PNUSAE018099, whole genome shotgun sequencing.project 182 rc linear DNA This entry is the master record for a whole genome shotgun sequencing project and contains no sequence data. Accession: AAADQP000000000.2 GI: 1820559580 Assembly. Search details txid562 [ Organism Genetic

f = c n cbi.nlm.nih.gov/protein 3 NCBI Resources How To Sign in to NCBI Protein Protein Search txid562[Organism] Create alert Advanced Help COVID-19 is an emerging, rapidly evolving situation. Get the latest public health information from CDC: https://www.coronavirus.gov. Get the latest research from NIH: https://www.nih.gov/coronavirus. Get the late Summary - 200 per page - Sort by Default order Send to: Filters: Manage Filters Species Bacteria (57,185,388) Archaea (36) Customize ... See the results of this search (5124985 items) in our new Identical Protein Groups database. Items: 1 to 200 of 57185393 Source databases PDB (32,438) RefSeq (3,610,367) UniProtKB/Swiss- Prot (23,143) Customize ... Results by taxon Top Organisms Tree] Escherichia coli (56915750) Enterobacteriaceae (57153291) Escherichia (56975025) enterobacteria (57164673) g-proteobacteria (57172774) All other taxa (12631) << First < Prev Page 1 of 285927 Next > Last >> More... Sul1.(plasmid (Escherichia coli] 308 aa protein Accession: QIK02129.1 GI: 1820521044 GenPept identical Proteins FASTA Graphics Genetic compartments Plasmid (433,531) Find related data Database: Select Sequence length Custom range... catB2 (plasmid) [Escherichia coli] 210 aa protein Accession: QHV83316.2 GI: 1820521043 GenPept identical Proteins FASTA Graphics Find items Molecular weight Custom range... Release date Custom range... aadA1 (plasmid) [Escherichia coli] 263 aa protein Search details txid562 [ Organism

Answer 2:

a. Scientific name for Plague thrips is Thrips imaginis.

b. There are 16 sequence records have been found.

c. Mitochondrial genome, EF1, COI genes and genes for 5.8S rRNA, ITS2, 28S rRNA have been sequenced.

d. Author - Nguyen,D.T., Spooner-Hart,R.N. and Riegler,M.

Year - 2015

Title - Polyploidy versus endosymbionts in obligately thelytokous thrips

Journal - BMC Evolutionary Biology 15 (1), 23 (2015)

Answer 3:

a. 5 Publications of Thanh NM were deposited in PubMed.

b. 2 aquatic animals are :- Striped catfish (Pangasianodon hypophthalmus), and Giant freshwater prawn (Macrobrachium rosenbergii)

c.Title: Voltammetry Determination of Pb(II), Cd(II), and Zn(II) at Bismuth Film Electrode Combined with 8-Hydroxyquinoline as a Complexing Agent.

Journal: Journal of analytical methods in chemistry

Year: 2019

Link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6636451/

Answer 4:

https://www.ncbi.nlm.nih.gov/genome/51?report=docsum