Workflows - Functional Annotation
RAMMCAP (Rapid Analysis of Multiple Metagenomes with a Clustering and Annotation Pipeline):
Use the full RAMMCAP pipeline for analysis of metagenomic sequences. It accepts a FASTA file of raw reads. The pipeline identifies the tRNA, rRNA, and ORFs from the reads. It then performs clustering analysis on the reads and the ORFs. The ORFs are annotated against PFAM, TIGRFAM, and COG.
Function annotation (PFAM):
Use HMMR 3.0 to give function annotation to protein sequences (based on PFAM database). This workflow accepts a FASTA file as input and produces three output files: one is a table of hits on the PFAM database, the remaining two are the tables of corresponding GO and EC mapping.
Function annotation (COG):
Use rpsblast to give function annotation to protein sequences (based on COG database for prokaryotic proteins). This workflow accepts a FASTA file as input and produces four output files: Two are the brief and detailed tables of rpsblast hits. The final two are the statistical information of hits on families and classes.
Function annotation (KOG):
Use rpsblast to give function annotation to protein sequences (based on KOG database for eukaryotic proteins). This workflow accepts a FASTA file as input and produces four output files: two are the brief and detailed tables of rpsblast hits. The final two are the statistical information of hits on families and classes.
Function annotation (TIGRFAM):
Use HMMR 3.0 to give function annotation to protein sequences (based on TIGRFAM database). This workflow accepts a FASTA file as input and produces three output files: one is a table of hits on TIGRFAM database, the remaining two files are the tables of corresponding GO and EC mapping.
Function annotation (NCBI PRK):
Use rpsblast to give function annotation to protein sequences (based on PRK database Reference Sequence proteins). This workflow accepts a FASTA file as input and produces three output files: two are the brief and detailed tables of rpsblast hits. The final two are the statistical information of hits on families and classes.
Notes:
- To adjust default parameters, click on the “Advanced Parameters” tab on the workflow submission form.
- With exception to the full RAMMCAP workflow, currently these workflows do not have a graphical output. Please download the results to your local computer for viewing.