LccED database annotation
I learned that LccED is a database about lignin degradation. Recently, I have got a metagenome data and want to obtain the information of lignin degradation. So, I want to get my data annotated against the LccED database. But, I have some questions:
1 Does it deal with one sequence at one time? Or it can process in batch?
2 I have ~272,000 predicted ORFs which are saved in a file format of .fna (a fasta file including the predicted sequences). How can I compare them against LccED database at once? Can I compare all of them through uploading the file?
I’m looking to forward to hearing from you! Many thanks!
#Reply: You can download the sequences from the sequence browser for a given superfamily at once in a single FASTA file, as a starting point for your own analyses (e.g. to create your own local BLAST database, etc.)