1 / 124

A Field Guide part 2

National Center for Biotechnology Information. A Field Guide part 2. UT-Health Science Center. February 14, 2006. Header. Feature Table. Sequence. GenBank Records. The Flatfile Format. LOCUS NM_019570 4279 bp mRNA linear INV 28-OCT-2004

colton
Download Presentation

A Field Guide part 2

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript


  1. National Center for Biotechnology Information A Field Guidepart 2 UT-Health Science Center February 14, 2006

  2. Header Feature Table Sequence GenBank Records The Flatfile Format

  3. LOCUS NM_019570 4279 bp mRNA linear INV 28-OCT-2004 DEFINITION Mus musculus REV1-like(S. cerevisiae)(Rev1l),mRNA ACCESSION NM_019570 VERSION NM_019570.3 GI:50811869 KEYWORDS . = Title A Typical GenBank Record

  4. GenBank Record: Feature Table

  5. GenBank Record: Feature Table, con’t. GenPept identifier

  6. skip GenBank Record: sequence

  7. [accn] [orgn] [mdat] [prop] Indexing for Nucleotide UID 59958365 FieldIndexed Terms [primary accession] NM_001012399 [title] Bos taurus hemochromatosis (hfe), mRNA. [organism] Bos taurus [sequence length] 1168 [modification date] 2005/02/19 [properties] biomol mrna gbdiv mam srcdb refseq

  8. Global Entrez Search: HFE HFE

  9. [Title] Entrez Nucleotide: HFE 137 records Not HFE

  10. 42 records Curated HFE splice variants (11 total) Smarter Query hfe[title] AND human[orgn]

  11. hfe[title]ANDhuman[orgn] (con’t) Primary data

  12. Preview/IndexGateway to Advanced Searches

  13. Preview/Index

  14. srcdb Preview/Index: Properties, srcdb Properties

  15. Preview/Index: Properties, srcdb …AND srcdb refseq[Properties]

  16. Preview/Index: Properties, srcdb …AND srcdb ddbj/embl/genbank[Properties]

  17. Primate division gbdiv pri[prop] EST division gbdiv est[prop] Database Queries #1hfe 137 #2 hfe[title]AND human[orgn] 42 #3 #2 AND srcdb refseq[prop] 11 #4 #2 AND srcdb ddbj/embl/genbank[prop] 31 #5 #4 AND gbdiv pri[prop] 29 #4 #4 AND gbdiv est[prop] 2

  18. Genomic DNA biomol genomic[prop] cDNA biomol mrna[prop] Molecule Queries #1hfe 116 #2 hfe[title]AND human[orgn] 42 #3 #2 AND biomol mrna[prop] 29 #4 #2 AND biomol genomic[prop] 13

  19. Entrez Nucleotide Reviewed RefSeqs with transcript variants: srcdb refseq reviewed[prop]ANDtranscript[title] AND variant[title] More Queries… Fields are database-specific

  20. Entrez Nucleotide Reviewed RefSeqs with transcript variants: srcdb refseq reviewed[prop]ANDtranscript[title] AND variant[title] Entrez Gene Topoisomerase genes from Archaea: topoisomerase[gene name]ANDarchaea[organism] Genes on human chromosome 2 with OMIM links 2[chromosome] ANDhuman[organism]AND“gene omim”[filter] Membrane proteins linked to cancer: “integral to plasma membrane”[gene ontology]ANDcancer[dis] More Queries… Fields are database-specific

  21. Genomic Biology UniGene E-PCR Map Viewer Trace Archive Genome Resources Genomic Biology

  22. Genomic Biology

  23. Gen Biol: Gen Resources

  24. Map Viewer – Genome Annotation Updates

  25. Gen Biol: Gen Resources

  26. Genome Projects: microb

  27. Genome Projects: microb 13 Eukaryotic Genome Sequencing Projects Selected: Complete – 0, Assembly – 2, In Progress - 11

  28. Gen Biol: Gen Resources

  29. Gen Biol: Gen Resources

  30. Gen Biol: Gen Resources

  31. Gen Biol: Gen Resources

  32. Gen Biol: Gen Resources

  33. E-PCR Map Viewer Trace Archive Genome Resources Genomic Biology UniGene

  34. UniGene Gene-oriented clusters of expressed sequences • Automatic clustering using MegaBlast • Each cluster represents a unique gene • Informed by genome hits • Information on tissue types and map locations • Useful for gene discovery and selection of mapping reagents

  35. A Cluster of ESTs query 5’ EST hits 3’ EST hits

  36. UniGene Collections

  37. UniGene Collections Species UniGene

  38. UniGene Hs build 188

  39. UniGene Cluster Hs.95351Lipase, hormone-sensitive (LIPE)

  40. UniGene Cluster Hs.95351

  41. UniGene Cluster Hs.95351: expression

  42. UniGene Cluster Hs.95351: seqs

  43. ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/ Get Sequences web page

  44. UniGene Map Viewer E-PCR Trace Archive Genome Resources Genomic Biology

  45. E-PCR Genomic sequence here

  46. Options

  47. Results

  48. reverse e-pcr

  49. reverse e-pcr

  50. reverse e-pcr

More Related