Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2016 Aug 25;113(37):10340–10345. doi: 10.1073/pnas.1605888113

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

PMC Copyright notice

Fig. S2. — TopGraph^MSA algorithm flowchart. (A) Nonredundant MSA is generated for a query sequence using BLAST, CD-HIT clustering, and MUSCLE alignment. For every possible segment $Δ G_{i n s e r t i o n}^{a p p}$ is calculated. Values different from the query’s $Δ G_{i n s e r t i o n}^{a p p}$ by more than 5 kcal/mol are discarded. The minimal value found is used as the weight for all edges leading to the segment’s node. The Bellman–Ford algorithm is applied to find the minimum energy topology. Using the minimal topology, constraints are derived for every chosen segment. A graph is rebuilt such that every segment found in the MSA is a constraint, and weights are assigned as the $Δ G_{i n s e r t i o n}^{a p p}$ of the corresponding query sequence. The Bellman–Ford algorithm (28) is used again to find the minimal energy topology.