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

Note: Only the first four questions/parts can be answered at once. Therefore ( question 1- a,b and question2 a,b ) are answered properly.

Question 1:

A)

1) Homos sapiens - Human

2) Heterodoxus macropus - wallaby louse

€ → C .ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=info&id=9606&Ivl=3&lin=f&keep=1&srchmode=1&unlock 3 NCBI POSTAL Taxonomy Browser Nucleotide Protein as complete name lock Go Clear Genome Structure PMC Taxonomy BioCollections Entrez PubMed Search for Display 3 levels using filter: none Homo sapiens Taxonomy ID: 9606 (for references in articles please use NCBI:txid9606) - current name Homo sapiens Linnaeus, 1758 Genbank common name: human NCBI BLAST name: primates Rank: species Genetic code: Translation table 1 (Standard). Mitochondrial genetic code: Translation table 2 (Vertebrate Mitochondrial) Other names: common name(s)- man Entrez records Database name Subtree links Direct links Nucleotide 27,606,488| 27,605,108 Protein 1,373,626 1,373,197 Structure 45,929 45,925 Genome Popset 24,377 24,376 SNP 686,600,501 686,600,501 Conserved Domains 50 GEO Datasets 1,929,978 1,929,978 PubMed Central 35,773 35,721 Gene 225,355 225,282 HomoloGene 18,713 18,713 SRA Experiments 1,912,998 1,912,427 GEO Profiles 61,958,910 61,958,910 Protein Clusters Identical Protein Groups 1,218,615 1,218,545 Bio Project 56,378 56,347 Bio Sample 5,131,268 5,131,062 Bio Systems 3,077 3,077 Assembly 366 366 db Var 5,904,686 5,903,353 Genetic Testing Registry 61,117| 61,117 Probe 27,382,497 27,382,497 Lineage( full) cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires, Primates; Haplorrhini; Simiiformes; Catarrhini; Hominoidea: Hominidae; Homininae; Homo 13

3) E.Coli - E.Coli

+ → C ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=145266 3 NCBI POOL - Taxonomy Browser Nucleotide Protein as complete name lock Go Clear Genome Structure PMC Taxonomy BioCollections Entrez PubMed Search for Display 3 levels using filter: none Heterodoxus macropus Taxonomy ID: 145266 (for references in articles please use NCBI:txid145266) r current name Heterodoxus macropus Genbank common name: wallaby louse NCBI BLAST name: lice Rank: species Genetic code: Translation table 1 (Standard). Mitochondrial genetic code: Translation table 5 (Invertebrate Mitochondrial). Entrez records Database name Direct links Nucleotide Protein Genome PubMed Central Gene Identical Protein Groups Bio Project Taxonomy MI Lineage( full ) cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Paraneoptera; Psocodea; Phthiraptera; Amblycera; Boopidae; Heterodoxus External Information Resources (NCBI LinkOut) LinkOut Provider LinkOut Show Biotic Interactions plazi Subject taxonomy/phylogenetic taxonomy/phylogenetic Global Biotic Interactions Plazi Notes: Groups interested in participating in the LinkOut program should visit the LinkOut home page. A list of our current non-bibliographic LinkOut providers can be found here. Information from sequence entries Show organism modifiers

→ C o ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=info&id=562&Ivl=3&lin=f&keep=1&srchmode=1&unlock 3 NCBI POST Taxonomy Browser Nucleotide Protein as complete name lock Go Clear Genome Structure PMC Taxonomy BioCollections Entrez PubMed Search for Display 3 levels using filter: none Escherichia coli 422 Taxonomy ID: 562 (for references in articles please use NCBI:txid562) - current name Escherichia coli (Migula 1895) Castellani and Chalmers 1919 type strain of Escherichia coli: ATCC:11775, CCUG:24, CCUG:29300, CIP:54.8, DSM:30083, JCM:1649, BCCM/LMG:2092, NBRC:102203, NCCB:54008, NCTC:9001, IAM:12119 homotypic synonym: "Bacillus coli" Migula 1895, effective name 1). "Bacterium coli" (Migula 1895) Lehmann and Neumann 1896, effective name 1) Enterococcus coli includes: Escherichia sp. 3_2_53FAA equivalent: Escherichia/Shigella coli NCBI BLAST name: enterobacteria Rank: species Genetic code: Translation table 11 (Bacterial, Archaeal and Plant Plastid) Other names: heterotypic synonym "Bacterium coli commune" Escherich 1885, effective name 1) Entrez records Database name Subtree links Direct links Links from type Nucleotide 7,665,217 6,455,821 Protein 57,094,303 45,115,036 Structure 2,784 5,631 Genome Popset 1 5,214 5,204 Conserved Domains 48 29 GEO Datasets 14,847 8,828 PubMed Central 316,126 316,121 Gene 363,980 44,724 SRA Experiments 153,817 134,391 GEO Profiles 313,301 298,677 Protein Clusters 17,571 17,571 Identical Protein Groups|5,070,256 4,760,253 Bio Project 7,786 4.323 Bio Sample 164,801 146,110 Bio Systems 22,561 1,814 Assembly 23,774 19,952 Probe 2,210 1,804 PubChem BioAssay 16,622 14,911 Taxonomy 3,324 -common name(s)— E. coli Lineage( full) cellular organisms; Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Escherichia Notes:

Part B)

1) Homo Sapiens Nucleotides - 27613709

+ → C o ncbi.nlm.nih.gov/nucleotide?term=txid9606[Organism] 3 NCBI Resources How To Sign in to NCBI Nucleotide Nucleotide Search txid9606[Organism] Create alert Advanced Help Summary - 20 per page - Sort by Default order Send to: - Filters: Manage Filters Species Animals (27,556,432) Viruses (4,545) Customize ... Next > Last >> Molecule types genomic DNA/RNA (15,212,524) mRNA (9,796,790) rRNA (46) Customize ... Items: 1 to 20 of 27613709 << First <Prev Page 1 of 1380686 O Homo sapiens HLA-A gene for MHC class I antigen, partial cds, allele: HLA-A*66:05 1. 1,022 bp linear DNA Accession: LC533107.1 GI: 1820736259 GenBank FASTA Graphics Results by taxon Top Organisms [Tree] 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) Homo sapiens HLA-C gene for MHC class I antigen, partial cds, allele: HLA-C*JRC-C-021 3. 1,696 bp linear DNA Accession: LC533105.1 GI: 1820736255 GenBank FASTA Graphics Search details txid9606[Organism] Genetic compartments Mitochondrion (184,127) Plasmid (102) Plastid (3) Homo sapiens HLA-C gene for MHC class I antigen, partial cds, allele: HLA-C*JRC-C-020 1,022 bp linear DNA Accession: LC533104.1 GI: 1820736253 GenBank FASTA Graphics Sequence length Custom range... Search See more... Release date Custom range... Homo sapiens solute carrier family 66 member 1 like (SLC66A1L), transcript variant 3, non-coding 5. RNA 1,150 bp linear transcribed-RNA Recent activity Turn Off Clear Revision date

1) Homo Sapiens Proteins - 1380761

2) Heterodoxus macropus Nucleotides - 02

c n cbi.nlm.nih.gov/protein?term=txid9606[Organism] 3 NCBI Resources How To Sign in to NCBI Protein Protein txid9606[Organism] Create alert Advanced Search Help 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 [Tree] 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) RefSeg (113,568) UniProtKB/Swiss- Prot (20,452) Customize ... 1. MHC class I antigen, partial [Homo sapiens] 273 aa protein Accession: BCB28916.1 GI: 1820736260 GenPept Identical Proteins FASTA Graphics Find related data Database: Select 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 Custom range MHC class I antigen, partial [Homo sapiens) 365 aa protein Accession: BCB28914.1 GI: 1820736256 GenPept Identical Proteins FASTA Graphics Search See more... Release date Custom range... O 4. Revision date Custom range... MHC class | antigen, partial [Homo sapiens] 273 aa protein Accession: BCB28913.1 GI: 1820736254 GenPept Identical Proteins FASTA Graphics Recent activity Turn Off Clear a txid9606[Organism] (1380761) Protein Clear all Q Homo sapiens (1) Show additional filters 5-hydroxytryptamine receptor 2A isoform 1 Homo sapiens Taxonomy

2) Heterodoxus macropus Proteins - 26

f = c n cbi.nlm.nih.gov/nucleotide?term=txid 145266[Organism] 3 NCBI Resources How To Sign in to NCBI Nucleotide Nucleotide Search txid145266[Organism]|| Create alert Advanced Search Help 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 ... Heterodoxus macropus mitochondrion, complete genome 14,670 bp circular DNA Accession: AF270939.1 GI: 12328587 Protein PubMed Taxonomy GenBank FASTA Graphics Source databases INSDC (GenBank) (1) RefSeq (1) Customize ... Find related data Database: Select Find items Sequence Type Nucleotide (2) 2. Heterodoxus macropus mitochondrion, complete genome 14,670 bp circular DNA Accession: NC_002651.1 Gl: 12383036 Bio Project Protein PubMed Taxonomy GenBank FASTA Graphics Genetic compartments Mitochondrion (2) Search details txid145266[Organism] Sequence length Custom range. Search See more... Release date Custom range. Revision date Custom range... Recent activity Turn Off Clear Clear all Q txid 145266[Organism) (2) Nucleotide Show additional filters a txid9606[Organism) (27613709) Nucleotide homo sapiens (1)

3) E.Coli - Nucleotide - 7749435

c n cbi.nlm.nih.gov/protein?term=txid 145266[Organism] 3 NCBI Resources How To Sign in to NCBI Protein Protein txid 145266[Organism]| Create alert Advanced Search Search Help Summary - 20 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 RefSeq (13) Customize ... Items: 1 to 20 of 26 Find items << First < Prev Page 1 of 2 Next > Last >> Genetic compartments Mitochondrion (26) O ATP synthase 8 (mitochondrion) [Heterodoxus macropus 53 aa protein Accession: AAG52657.1 GI: 12328600 Nucleotide PubMed Taxonomy GenPept Identical Proteins FASTA Graphics Search details txid145266[Organism] Sequence length Custom range... Molecular weight Custom range... Search See more... 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 Revision date Custom range... Recent activity Turn Off Clear Clear all Q txid 145266[Organism) (26) Protein Show additional filters cytochrome oxidase subunit II (mitochondrion) [Heterodoxus macropus 219 aa protein Accession: AAG52655.1 GI: 12328598 Nucleotide PubMed Taxonomy GenPept Identical Proteins FASTA Graphics Q txid9606[Organism] (27613709) Nucleotide a homo sapiens (1) Taxonomy NADH dehydrogenase subunit 3 (mitochondrion [Heterodoxus macropus 108 aa protein Accession: AAG52654.1 GI: 12328597 Nucleotide PubMed Taxonomy Heterodoxus macropus mitochondrion, complete genome Nucleotide Homo sapiens (1)

3) E.Coli - Proteins - 57185393

€ → c n cbi.nlm.nih.gov/nucleotide?term=txid562[Organism] 2 NCBI Resources How To U Sign in to NCBI Nucleotide Nucleotide Search txid562[Organism]|| Create alert Advanced Search Help Summary - 20 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 20 of 7749435 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) More... << First <Prev Page 1 of 387472 Next > Escherichia coli strain 643226, whole genome shotgun sequencing project 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 Find related data Database: Select Source databases INSDC (GenBank) (4,273,805) RefSeq (3,470,629) Customize ... 2. 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 GenBank Search details txid562[Organism] Genetic compartments Chloroplast (2) Plasmid (25,407) Plastid (2) 3. Search Escherichia coli strain PNUSAE018214, whole genome shotgun sequencing project 395 rc linear DNA This entry is the master record for a whole genome shotgun sequencing project and contains no sequence data. Accession: RMNC00000000.2 GI: 1820559578 Assembly GenBank See more... Sequence length Custom range. Recent activity Release date Custom range.. Turn Off Clear

→ cbi.nlm.nih.gov/protein?term=txid562[Organism] 3 NCBI Resources How To Sign in to NCBI Protein Protein txid562[Organism]|| Create alert Advanced Search Help Summary - 20 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 20 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) More... << First <Prev Page 1 of 2859270 Next > Last >> 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 O 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 Accession: QHV83315.2 GI: 1820521042 GenPept identical Proteins FASTA Graphics Search details txid562[Organism] Revision date Custom range.. Clear all Search See more.. Show additional filters aph(3')-XV (plasmid) [Escherichia coli] 264 aa protein Accession: QHV83314.2 GI: 1820521041 GenPept Identical Proteins FASTA Graphics Recent activity O VIM-1 (plasmid) [Escherichia coli] Turn Off Clear

Question 02:

a)

Scientific name of plague thrips -

 Thrips imaginis

c n cbi.nlm.nih.gov/nuccore/AF335993.2, ☆ ABPG 3 NCBI Resources How To Sign in to NCBI Nucleotide Nucleotide Search Advanced Help GenBank Send to: Change region shown Customize view Thrips imaginis mitochondrion, complete genome GenBank: AF335993.2 FASTA Graphics Go to: Analyze this sequence Run BLAST Pick Primers Highlight Sequence Features Find in this Sequence Related information Protein PubMed LOCUS AF335993 15407 bp DNA circular INV 24-JUL-2016 DEFINITION Thrips imaginis mitochondrion, complete genome. ACCESSION AF335993 VERSION AF335993.2 KEYWORDS SOURCE mitochondrion Thrips imaginis (plague thrips) ORGANISM Thrips imaginis Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Paraneoptera; Thysanoptera; Terebrantia; Thripoidea; Thripidae; Thrips. REFERENCE 1 (bases 1 to 15407) AUTHORS Shao, R., Campbell,N.J., Schmidt, E.R. and Barker,s.c. TITLE Increased rate of gene rearrangement in the mitochondrial genomes of three orders of hemipteroid insects JOURNAL Mol. Biol. Evol. 18 (9), 1828-1832 (2001) PUBMED 11504862 REFERENCE 2 (bases 1 to 15407) AUTHORS Shao, R. and Barker,s.c. TITLE The highly rearranged mitochondrial genome of the plague thrips, Thrips imaginis (Insecta: Thysanoptera): convergence of two novel gene boundaries and an extraordinary arrangement of rRNA genes JOURNAL Mol. Biol. Evol. 20 (3), 362-370 (2003) PUBMED 12644556 REFERENCE 3 (bases 1 to 15407) AUTHORS Shao, R., Campbell,N.J.H., Schmidt, E.R. and Barker, s.c. Taxonomy Full text in PMC Gene PubMed (Weighted) LinkOut to external resources BOLD Link (GBMH0311-06] [Barcodes of Life]

b) We found 14 sequence records

f = c n cbi.nlm.nih.gov/nucleotide?term=txid159957[Organism] 3 NCBI Resources How To Sign in to NCBI Nucleotide Nucleotide Search txid 159957[Organism] Create alert Advanced Help Summary - 20 per page - Sort by Default order Send to: - Filters: Manage Filters Species Animals (14) Customize ... Items: 14 Analyze these sequences Run BLAST Molecule types genomic DNA/RNA (14) Customize ... Thrips imaginis isolate Ti-104 cytochrome oxidase subunit I (COI) gene, partial cds; mitochondrial 658 bp linear DNA Accession: HM246169.1 GI: 303292738 Protein Taxonomy GenBank FASTA Graphics PopSet Source databases INSDC (GenBank) (13) RefSeq (1) Customize ... Find related data Database: Select Find items Sequence Type Nucleotide (14) Thrips imaginis mitochondrion, complete genome 2. 15,407 bp circular DNA Accession: AF335993.2 Gl: 24762254 Protein PubMed Taxonomy GenBank FASTA Graphics Genetic compartments Mitochondrion (4) Search details txid159957[Organism] Sequence length Custom range. Thrips imaginis isolate Ti1 elongation factor 1 alpha (EF1a) gene, exons 1, 2 and partial cds 3. 851 bp linear DNA Accession: KM582808.1 GI: 823227376 Protein PubMed Taxonomy GenBank FASTA Graphics Search See more... Release date Custom range. Revision date Custom range... Recent activity Turn Off Clear Clear all a txid 159957[Organism] (14) Thrips imaginis genes for 5.8S rRNA, ITS2, 28S rRNA, partial and complete sequence, specimen voucher: NCHU:Qua125-1 455 bp linear DNA Accession: AB775432.1 GI: 743965723 PubMed Taxonomy GenBank FASTA Graphics Nucleotide Show additional filters Q Taxonomy Links for Nucleotide (Select 24762254) (1) Taxonomy Thrips imaginis mitochondrion, complete F