• E-mail address

The e-mail address is used to return the web link for the output once the job finishes.
 
• Paste your protein sequence

The protein sequence of interest needs to be entered into this box in one letter amino acid codes.
 
• Upload your sequence file

Alternatively, the sequence of interest can be uploaded in FASTA format.
 
• Perform a PSI-BLAST search

If user does not provide a BLAST output, BlastProfiler will perform a PSI-BLAST search.

Either PDB or NR database can be selected for searching. The number of iterations can be selected to be between 1 to 4.
 
• Upload PSI-BLAST output file

Alternatively, user can upload a raw BLAST/PSI-BLAST output. BlastProfiler will not perform a new PSI-BLAST search in this case.
 

• Minimum sequence identity between each hit and query

Only those hits that have a higher sequence identity with query than this cutoff will be selected.
 
• Maximum sequence identity between each hit and query

Only those hits that have a lower sequence identity with query than this cutoff will be selected.
 
• Maximum e-value for each hit

Only those hits that have a more significant (smaller) BLAST/PSI-BLAST e-value than this cutoff will be selected.
 
• Minimum percentage of sequence overlap between each hit and query

Only those hits that have a higher percent sequential overlap than this cutoff will be selected.
 
• Minimum length of sequence overlap between each hit and query

Only those hits that have a larger residue overlap with query than this cutoff will be selected.
 
• Maximum sequence identity between pairs of aligned sequence hits

Sequence clustering is performed using CD-HIT at this cutoff value and only one member (the longest sequence) is kept from each cluster.
 

• Raw Sequences

Output consists of a list of sequences in one letter amino acid codes in either FASTA or PIR format.
 
• Alignment

Output consists of a multiple sequence alignments compiled from pairwise BLAST alignments of each hit and the query. The alignment can be obtained in FASTA, PIR or CLUSTALW format.
 
• Realign sequences with CLUSTALW

All hit sequences are realigned with CLUSTALW in one multiple sequence alignment. The multiple sequence alignment can be obtained in CLUSTALW, PIR, FASTA or PHYLIP format.