searching for sequences at ncbi: blastsearching for sequences at ncbi:-gene-based entrez,...

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1 Searching for sequences at NCBI: -Gene-based Entrez, Nucleotide, Protein BLAST -Organism-based Taxonomy Browser PopSet (Population Sets) * * * * * * These are text- based searches! Not sequence similarity! Are these guaranteed to be orthologs? Use BLAST to bring in more sequences.

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Page 1: Searching for sequences at NCBI: BLASTSearching for sequences at NCBI:-Gene-based Entrez, Nucleotide, Protein BLAST-Organism-based Taxonomy Browser PopSet (Population Sets) * * * *

1

Searching for sequences at NCBI:-Gene-based

Entrez, Nucleotide, ProteinBLAST

-Organism-basedTaxonomy BrowserPopSet (Population Sets)

*

*

*

*

**

These are text-based searches!

Not sequencesimilarity!

Are theseguaranteed tobe orthologs?

Use BLAST to bring in more sequences.

Page 2: Searching for sequences at NCBI: BLASTSearching for sequences at NCBI:-Gene-based Entrez, Nucleotide, Protein BLAST-Organism-based Taxonomy Browser PopSet (Population Sets) * * * *

2

Organism-based Searching

-Taxonomy browser-PopSet

*

Page 3: Searching for sequences at NCBI: BLASTSearching for sequences at NCBI:-Gene-based Entrez, Nucleotide, Protein BLAST-Organism-based Taxonomy Browser PopSet (Population Sets) * * * *

3

within speciespolymorphismis also found inPopSet

Page 4: Searching for sequences at NCBI: BLASTSearching for sequences at NCBI:-Gene-based Entrez, Nucleotide, Protein BLAST-Organism-based Taxonomy Browser PopSet (Population Sets) * * * *

4

Use BLAST to bring in more sequences.

NCBI Field Guide NCBI Molecular Biology Resources March 2007 NCBI Databases

NCBI FieldGuide NCBI Molecular Biology Resources March 2007 Peter Cooper Using NCBI BLAST

Protein database ..... of NCBI

NCBI resources II: web-based tools and ftp resourcesbcb.unl.edu/yyin/teach/PBB/ncbi-blast.pdf · • NCBI Genomes – NC_ RefSeqs – GenBank Chromosomes • dbest – EST Division

MYNCBI-LOG · NCBI Resources How To (9 Sign in to NCBI My NCBI retains user information and database preferences to provide customized services for many NCBI databases. Goole and

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L10 NCBI Exercises

Two Examples of Datanomic - DTCProvenance of sequences downloaded from NCBI on a nightly basis Every night a cron job is run to check for the NCBI release of new Medicago genome sequences

Ncbi basic intro_v_pitt_kent_osu

NCBI Help Manuel 5

NCBI Review Concepts 20040715 Chuong Huynh. NCBI Pairwise Sequence Alignments Purpose: identification of sequences with significant similarity to (a)

NCBI PubMed Introductory Overview. NCBI PubMed The National Institutes of Health Bethesda, MD

Biology 4900 Biocomputing. Chapter 4 BLAST BLAST BLAST allows user to search a sequence (the query) against millions of sequences in the NCBI database

oseosarcoma ncbi

SUPPLEMENT 1: Table of protein sequences and associated NCBI

NCBI FieldGuide NCBI Molecular Biology Resources Part 2 November 2008 Peter Cooper

NCBI Molecular Biology Resources

XWRAPComposer - ecology labfaculty.cse.tamu.edu/caverlee/pubs/liu06xwrap.pdfservice, such as NCBI Blast Web service, that will return homologs (other genes with similar sequences)

My NCBI USMP 2011

Primary databases ncbi

A nemertean excitatory peptide/CCHamide regulates ciliary ......topsis capensis (NCBI: SRR1145776), Priapulus caudatus (NCBI: SRR1212719), Rotaria tardigrade (NCBI: SRR24 30032),Tubulanus

Bioinformatics Web Resources NCBI / EBI / Uniprot / … · Bioinformatics Web Resources NCBI / EBI / Uniprot / Pfam • Recognizing web addresses (URLs) • NCBI –eutilities: esearch/efetch/blast

NCBI FieldGuide NCBI Molecular Biology Resources March 2007 Using Entrez

Introduction to NCBI

Clean up sequences with multiple >GI numbers when downloaded from NCBI BLAST website [ Example of one sequence and the duplication clean up for phylo tree

NCBI FieldGuide NCBI Molecular Biology Resources January 2008 Peter Cooper Using NCBI BLAST