The databases to run the sequence similarity search against. Multiple databases can be selected at the same time.
Provide sequence in GCG, FASTA, GenBank, PIR, NBRF, PHYLIP, or UniProtKB/Swiss-Prot format directly, or upload a file.
Select the iteration program
Expectation value threshold for automatic selection of matched sequences for inclusion in the PSSM at each iteration.
Maximum number of iterations
Select method to mask sequence regions for HOEs in PSSM constructions. This option allows you to mask sequence characters beyond the alignment region when constructing the PSSM, reducing over-extension errors.
Produce domain annotation for query, subject or both
The source domain database
Domain diagram display
Sequence boundaries for PSSM
Domain Q-value threshold
The comparison matrix to be used to score alignments when searching the database.
Penalty taken away from the score when a gap is created in sequence. Increasing the gap opening penalty will decrease the number of gaps in the final alignment.
Penalty taken away from the score for each base or residue in the gap. Increasing the gap extension penalty favours short gaps in the final alignment, conversly, decreasing the gap extension penalty favours long gaps in the final alignment.
Limits the number of scores and alignments reported based on the expectation value. This value is the maximum number of times the match is expected to occur by chance.
Maximum number of alignment score summaries reported in the result output.
Maximum number of alignments reported in the result output.
Display of multiple high-scoring alignments (HSPs)
Different score formats.
Turn on/off the histogram in the PSI-Search result. The histogram gives a qualitative view of how well the statistical theory fits the similarity scores calculated by the program.
Checkpoint file from the previous iteration. Must be in ASN.1 Binary Format.