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Figure 4 | BMC Evolutionary Biology

Figure 4

From: FlowerPower: clustering proteins into domain architecture classes for phylogenomic inference of protein function

Figure 4

The FlowerPower algorithm. "Q" indicates the query (or seed) sequence. Sequences sharing the same domain structure are indicated as blue stars; all other sequences are indicated as brown triangles. SCI-PHY subfamilies are indicated by black ovals. 1. Identify a set of potential homologs S using PSI-BLAST; filter to remove much longer or much shorter sequences. 2. Select a core set for initial alignment. 3. Identify subfamilies using SCI-PHY and construct subfamily HMMs (SHMMs). 4. Score S with the SHMMs, and identify those sequences receiving scores with E-values below cutoff. Align each sequence to its closest SHMM. Evaluate the alignment with user-specified criteria; remove sequences that do not meet these criteria. 5. Run SCI-PHY on the new alignment to identify subfamilies and construct SHMMs. 6. Repeat steps 1–5 until convergence.

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