RAMMCAP – Rapid clustering and functional annotation for metagenomic sequences
Taxonomy / population analysis
ORF and cluster annotation
Pfam, Tigrfam, COG, etc.
Very fast (10-100x) as compared to BLAST-based methods
Effective tools: CD-HIT, HMMERHEAD, meta_RNA, and RPS-BLAST
Focused functional annotation via curated protein families
CD-HIT, 90-95% More in-depth analysis and further annotation Metagenomic Raw reads CD-HIT-EST, 95% DNA clusters Protein clusters Representative sequences Unique DNA sequences ORF Annotation 1. ORF_finder 2. Metagene CD-HIT, 60 or 30% COG Pfam Tigrfam HMMER HMMERHEAD RPS-BLAST Cluster Annotation 1. tRNA scan 2. rRNA scan 3. meta_RNA ORFs Non-redundant ORFs tRNAs rRNAs
Annotation workflow A green box is called an ‘actor’ , which performs a task. This special actor represents an annotation component, such as BLAST search. Workflow parameters, which can be specified by users in the portal, are passed to workflow components. Data flow is divided.
Run branches within workflow A ORF clustering branch A functional annotation branch