Hi, I need help. I have the genome, only the nucleotide sequence, of lens ervoides (legume) and need to find genes and symbiosis protein sequences associated with rhizobia using known protein sequences in other legumes. How do i start?
Is the genome for your legume in the public domain? If so, then use a BLAST search with the protein sequences from other legumes as your query against the genome of your legume.
You might look at the methods used in this paper:Article A genome-wide identification and comparative analysis of the...
They look for a different class of genes (mildew resistance), but the methods are the same.
In general, if you have protein sequences from other species, you can use TFastA or TBlast for homologous sequences in all six reading frames. Of course, if you look at genomic data, the genes will be interrupted by introns.
You can use Blastp to TBlastn at https://knowpulse.usask.ca/genome-assembly/Lens%20ervoides%3A%20IG%2072815%20Genome%20Assembly%201.0
Use BLAT. you can follow this protocol: Article Using BLAT to Find Sequence Similarity in Closely Related Genomes
great. Thanks for the help. Now my problem is this: i have the blast results that indicate the nucleotide when starts the cds. But i only have the nucleotide sequences of lens ervoides, the whole genome. How can i extract this region?
- Badges
- Science topic
- Similar topics
- Physical Sciences
- Physical Phenomena
- Luminescence
- Fluorescence