Post Reply 
 
Thread Rating:
  • 0 Votes - 0 Average
  • 1
  • 2
  • 3
  • 4
  • 5
Why do start coordinates differ by 1 base
19-Nov-2013, 05:21 PM
Post: #1
Why do start coordinates differ by 1 base
Hello,

S.cerevise YAL012W CDS starts at genomic coordinate:
130799: according to the header of the FASTA format sequence
130798: according to the sgdGene annotated table (http://gwips.ucc.ie/cgi-bin/hgTables)

* according to the NCBI the start genomic coordinate of this gene is: 130799 (ftp://ftp.ncbi.nlm.nih.gov/genomes/Fungi...1133.ptt).

Best Regards,
Renana


Hello Renana,

Regarding the start genomic coordinate for this gene (and for all genes), out tables use the UCSC Genome Browser table representations where start coordinates are 0-based (eg 130798 for YAL012W), and are converted to 1-based coordinates for display (eg 130799 for YAL012W). I refer you to the section "Database/browser start coordinates differ by 1 base" in the following FAQ from the UCSC Genome Browser https://genome.ucsc.edu/FAQ/FAQtracks.html.

I hope this answers your question regarding the differences in start coordinates for the different information displays.

Thanks again for your interest in GWIPS-viz.

Kind Regards,
Audrey
Find all posts by this user
Quote this message in a reply
Post Reply 


Forum Jump:


User(s) browsing this thread: 1 Guest(s)

GWIPS-viz | Return to Top | Return to Content | Light (Archive) Mode | RSS Syndication