FlowerPower
FlowerPower is a protein homology clustering algorithm, similar to PSI-BLAST in its iterated approach to alignment, profile construction, and homolog identification, but with distinct differences. FlowerPower includes phylogenetic tree construction, subfamily identification, and subfamily HMM construction in the clustering and alignment process. This enables FlowerPower to avoid some of the common pitfalls of protein clustering methods (particularly profile drift). FlowerPower can also be parameterized for use in phylogenomic analysis for protein functional classification, where global-global alignment of all proteins in the set is required for accuracy of molecular function inference.
An overview of the FlowerPower method is available here.
FASTA format
FASTA format is described here.
Typically, a FASTA format sequence consists of a line beginning
with a ">" that provides the sequence name or description,
followed by one or more lines with one-letter amino acid ("residue")
codes.
Upload FASTA file
Alternatively, sequences in a file on your local computer may be used
as the input seed.
The sequence file must be in
fasta format.
Send email to
Email will be sent to this address announcing completion of the FlowerPower run. The email will provide a URL link to the results.
Number of SHMM iterations
This sets the number of times the homologs resulting from a PSI-BLAST search are searched by FlowerPower with subfamily Hidden Markov Models. The default is 3. Users should note that increasing this parameter slows down the program.
Maximum e-value for inclusion of sequences default: depends on sequence length
By default, the e-value will be set as follows:
Sequence length less than 65: 1.0e-2;
Sequence length less than or equal to 100: 1.0e-3;
Sequence length greater than 100: 1.0e-4.
Number of PSIBLAST iterations
The number of PSI-BLAST iterations that FlowerPower will perform within
each FlowerPower iteration.