At present, the sequence input limit for first three (faster) classifiers is 2000 sequences.
For PSI-BLAST based prediction, limit is 100 sequences.
Due to PSI-BLAST searches against the NR-database and their corresponding conversion to PSSM matrices, the current limit for hybrid-based (best) classifier is 10 sequences / submission. For larger analysis, please contact us.
Each sequence should be at least more than 20 residues in length. The shorter sequence might be a "fragment" and so, the prediction will not make any sense.
Detailed description of the FASTA format is available at