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Lichtarge Computational Biology Lab

Houston, Texas

Lichtarge Computational Biology Lab
Lichtarge Computational Biology Lab
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Step 2: Enter input.


(Load example input)

Enter short name or ID (Reference sequence will be named query_ID):

Enter or paste the amino acid sequence in FASTA format below. Only the one-letter codes of the 20 standard amino acids, upper or lower case (ARNDCEQGHILKMFPSTWYVarndceqghilkmfpstwyv), will be accepted:

Show Advanced Options
Advanced Input and Parameters (Optional)
Trace Options
Real-Valued Trace (rvET)  
Position-specific gap-reducing real-valued trace  
BLAST
E-value cutoff:
Number of proteins to extract:
Use PSI-BLAST  
Number of PSI-BLAST iterations:
Use all sequences from all iterations of PSI-BLAST  
BLAST Database Options
Custom NCBI 
Custom UniRef90 
Custom UniRef100 
Custom SwissProt reviewed 
Sequence Selection
Restrict BLAST hits to gi#'s:
Restrict BLAST hits to # proteins:
Restrict BLAST hits to minimum e-value:
Restrict BLAST hits to maximum e-value:
Restrict BLAST hits to minimum sequence identity:
Restrict BLAST hits to maximum sequence identity:
Restrict BLAST hits to minimum fractional length to query:
Alignment & Tree
Do not remove fragments  
Fractional length used to define fragments (in relation to the query in the alignment):
Do not remove identical sequences  
Do not remove short sequences  
Fractional length used to define short sequences (in relation to the query):
Tree File (NHX format):
Custom Sequence Input (if not using BLAST)
Alignment File (GCG format):
-Or- Sequences File (FASTA format):
Query name in input file (eg: query_1aca):

Note: The output will not include structure data.
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