1 / 14

1. C. briggsae sequence curation 2. SNP data handling

1. C. briggsae sequence curation 2. SNP data handling. What’s involved: ACeDB database (brigace) with gene models and alignments Curator to make changes, be point of contact for user submissions Upload all gene data each release to Sanger Scripts that can be generalized to any genome

aderes
Download Presentation

1. C. briggsae sequence curation 2. SNP data handling

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. 1. C. briggsae sequence curation2. SNP data handling

  2. What’s involved: ACeDB database (brigace) with gene models and alignments Curator to make changes, be point of contact for user submissions Upload all gene data each release to Sanger Scripts that can be generalized to any genome Sanger generates various flat files (brigpep) and integrates into build C. briggsae sequence curation SAB 2008

  3. Current curation: 175 changes so far Orthologues (personal communication) Protein families (chemoreceptors) Submit to EMBL every frozen release Few systematic problems with original gene set: 2324 Start_not_found 60 don’t start in frame=0 Sequence changes : 1 waiting C. briggsae sequence curation SAB 2008

  4. Curation tool add-on for transferring new CDS structure SAB 2008

  5. What’s involved: ACeDB database (snpace) contains all SNPs for all species Curator to make changes and be point of contact for user submissions Scripts to upload ace files to Sanger to be integrated in build process SNP curation SAB 2008

  6. Current curation: C. elegans: Large datasets in last year: 50906 pas* (CB4858) 112101 hw* (CB4856) Individually entered: 225 Personal communication Papers C. briggsae: Currently 58000 SNP curation SAB 2008

  7. Future plans: New web form for submission More robust error checking Web interface improvement SNP curation SAB 2008

  8. Current Variation report page SAB 2008

  9. SNP track visible on genome browser SAB 2008

  10. Old WashU SNP display SAB 2008

  11. Out of 100 Jigsaw(Twinscan) predictions checked: 81 (55) were predicted correctly 1 (0) correctly indicated a required change 10 (25) differed from the curated CDS 3 (7) merged/split genes incorrectly 3 (1) CDS where there was a pseudogene 1 (2) missed a gene entirely 1 (6) gene predicted where there was none nGASP gene predictions are good, but still not perfect SAB 2008

  12. Jigsaw genes for C. elegans SAB 2008

  13. Jigsaw merges two curated CDSs - transfer gene IDs Jigsaw curated SAB 2008

  14. Jigsaw correctly makes same change as curator to chemoreceptor curated Jigsaw history SAB 2008

More Related