Two CDD search services are available: CD-Search (8), for protein and nucleotide queries and Batch CD-Search (9), for multiple protein queries.
Sequences were annotated according to homologies to protein database searches using translated nucleotide sequences and direct nucleotide queries http://blast.ncbi.nlm.nih.gov/Blast.cgi.nih.gov/Blast.cgi
For nucleotide queries there is an initial gene prediction step (using MED-Start) to generate a proteome, although.
Blastn compares a nucleotide query sequence against a nucleotide database.
Comparison of blastn (search a nucleotide database using a nucleotide query) and tblastx searches (search translated nucleotide database using a translated nucleotide query).
3. BLASTN also compares nucleotide query sequences to a nucleotide database.
Blosum62 matrix was used for BLASTX (when searching against a protein database with a DNA query), TBLASTN (when searching for translated nucleotide databases with a protein query) and TBLASTX (when searching for translated nucleotide databases with a translated nucleotide query).
It is also possible to choose to run the application in BLASTN or TBLASTX mode, i.e. by searching nucleotide databases using a nucleotide query or by searching translated nucleotide databases using a translated nucleotide query, respectively.
The ACT comparison tool used the tblastx program which searches a translated nucleotide database using a translated nucleotide query.
We thus carried out a tblastx analysis to search a translated nucleotide database using a translated nucleotide query.
