Are you interested in searching for a chromosomal region in a genome, but don’t know how to write the correct query? The good news is that the NCBI Genome Data Viewer (GDV) now supports a much wider array of search options. Some examples are listed below:
- chr1:1,500,000-2,000,000
- chr2: 1.5M – 2M
- chr2: 1.5M-2,540.2K
- 2:1,500,000-2,000,000
- 3: 21.33M – 22.01M
- 3: 21.335M..21.337M
- chr1:1,500,000 / 200
- chr1:101,500,200
- 1:101,500,200
- 1:1,500K/0.5K
- chr5
- 10
You can use any of these queries or the ones described below for assembly aliases either on the GDV landing page or in the GDV search box (Figure 1).
Figure 1. The search boxes on the GDV landing page (left) and within the GDV graphical interface (right) showing queries with chromosome aliases for the domestic cat.
Non-human assemblies listed below now support a new feature for matching different chromosome aliases.
- American alligator
- Armadillo
- Olive baboon
- Pygmy chimpanzee (Bonobo)
- Budgerigar
- Small-eared galago
- C. elegans
- Domestic cat …and many more organisms!
For example, for cat, chromosome aliases that now map to chrE2 are NC_018737.3, CM001392.3, and E3. Search terms such as NC_018737.3:11440042..11440359 and CM001392.3:11,440,042..11,440,359 or E2:11440042-11440359 will be equivalent to chrE2:11440042-11440359.
Please try these out, or better yet, try your own queries and let us know what you think!