Output

Output

Mantis Output

This tool generates 3 tab-separated output files (along with HMMER's default output), the output_annotation.tsv,interpreted_annotation.tsv, and consensus_annotation.tsv:

The output_annotation.tsv will look something like this:

Query	HMM_file	HMM_hit	Query_length	Query_hit_start	Query_hit_end	HMM_hit_start	HMM_hit_end	evalue
Query_1	HMM_file_1	HMM_hit_1	154	64	90	85	105	2.1e-46

The output_annotation.tsv is not very informative when we need to connect our annotations to metadata, that's why I've included interpreted_annotation.tsv.

The interpreted_annotation.tsv will look something like this:

Query	HMM_file	HMM_hit	HMM_hit_accession	evalue	Query_length	Query_hit_start	Query_hit_end	HMM_hit_start	HMM_hit_end	I	Links
Query_1	HMM_file_1	HMM_hit_1	HMM_hit_accession_1	2.1e-46	230	50	80	300	340	I	pfam:link_1	enzyme_EC:link_1	description:free_text
Query_1	HMM_file_2	HMM_hit_2	HMM_hit_accession_2	3.9e-87	230	1	200	100	320	I	ko:link_1	enzyme_EC:link_2	description:free_text

See how are hits generated? to understand how Mantis is capable of capturing multiple matches for the same protein sequence within the same reference dataset. However, some query sequences may have different hits against our HMM sources, it is therefore necessary to find some sort of consensus between the several hits:

The consensus_annotation.tsv will look something like this:

Query	HMM_Files	HMM_Hits	Consensus_hits	Total_hits	I	Links
Query_1	HMM_file_1;HMM_file_2	HMM_hit_1;HMM_hit_2	3	3	I	pfam:link_1	enzyme_EC:link_2	description:free_text
Query_2	HMM_file_3;	HMM_hit_3	4	5	I	ko:link_1	description:free_text

The consensus coverage is the amount of hit sources that reached a consensus out of all the hit sources for the current query sequence (if there are 4 hits in the consensus and we had a total of 5 hits, then the consensus coverage is 4/5). If the consensus coverage is quite low, consider also taking a look at the results in the interpreted_annotation.tsv.
Note how each line now corresponds to a query sequence and how this query sequence can match against different HMM sources, thus having different HMM profile matches.
The consensus is not a mere agglomerate of all the matches found across the different HMM sources, it is actually a group of hits that form a consensus. Please see how are hit consensus generated? for more information.

Other outputs

Mantis also generates other output files and folders, these can be viewed to keep track of job's execution or HMMER's output files.

• domtblout: contains the domtblout files generated by HMMER
• output_hmmer: contains HMMER's console output
• Mantis.out: contains Mantis's console output