websites/dennogumi
websites/dennogumi
1
0
Fork 0
Code Releases Activity
dennogumi/content/post/2007-11-15-gene-identifiers.markdown
Luca Beltrame 64b24842b8
All checks were successful
continuous-integration/drone/push Build is passing
Details
Update all posts to not show the header text
2021-01-13 00:05:30 +01:00

1.1 KiB
Raw Blame History

author categories comments date header slug tags title omit_header_text disable_share wordpress_id
einar
Science
true 2007-11-15T19:57:16Z
image_fullwidth
banner_other.jpg
gene-identifiers
annotation
bioinformatics
microarray
python
Gene identifiers true true 336

While working today on an annotation class in Python I stumbled on a problem. Normally I work with lists of genes that are consistent, i.e. all Entrez Gene IDs (or RefSeq IDs, or Genome Browser IDs...), but today I had a list of mixed identifiers.

The subsequent idea was "let's implement auto-detection of common identifiers in the class". The problem is... is there any actual documentation on how identifiers are made? So far, using regular expressions, I've tracked down a few:

  • RefSeq

  • GenBank

  • Entrez Gene

  • UCSC Genome Browser

  • Ensembl

However, I have no idea if I have implemented all types of these IDs. Does anyone know a place where to look these information up?

(On a related note: my thesis defense will be on January 14th, 2008, so I have to get the printing going)