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Table 2 Annotation summary for example dataset

From: WebMGA: a customizable web server for fast metagenomic sequence analysis

Tool

Annotation Summarya

FNA-stat

Total reads: 555853, Length: 45~607, Average length: 251,

Total bases: 139813458, Total ambiguous bases: 96190,

Distribution of GC% and length in text files and in graphic files similar to Figure 2d

CD-HIT-EST

Parameters: "-d 0 -n 10 -l 11 -r 1 -p 1 -g 1 -G 0 -c 0.95 -aS 0.8"

Clusters: 419802, Size of the largest cluster: 69,

Clusters in CD-HIT format and in 'TAB' delimited text file,

Distribution of clusters in graphic file similar to Figure 2b

HMM-rRNA

rRNA sequences identified: 3858,

Archaeal-16S: 1, Eukaryotic-18S: 3, Bacterial-16S: 1347,

Bacterial-5S: 220, Bacterial-23S: 2285, Archaeal-5S: 2

tRNA-SCAN

tRNA sequences identified: 1378

Metagene

ORFs: 571261

FAA-stat

Total ORFs: 555853, Length: 20-121, Average length: 66,

Total letters: 37859696, Total ambiguous letters: 87294,

Distribution length in text file and in graphic file similar to Figure 2d

CD-HIT

Parameters: "-d 0 -n 5 -p 1 -g 1 -G 0 -c 0.9 -aS 0.8"

Clusters: 396559, Size of the largest cluster: 154,

Clusters in CD-HIT format and in 'TAB' delimited text file,

Distribution of clusters in graphic file similar to Figure 2b

COG

Parameters: "-e 0.001"

Total alignments: 199002, Total ORFs aligned: 198933,

Total COG families aligned: 2848, Total COG classes aligned: 23,

Alignments and derived results in 'TAB' delimited text files similar to Figure 2c

PFAM

Parameters: "-e 0.001"

Total alignments: 187156, Total ORFs aligned: 174115,

Total PFAM families aligned: 3131,

Total ORFs with GO annotation: 123294, Total GO terms annotated: 964

Total ORFs with EC annotation: 46207, Total EC terms annotated: 319

Alignments and derived results in 'TAB' delimited text files similar to Figure 2c

TIGRFAM

Parameters: "-e 0.001"

Total alignments: 6357, Total ORFs aligned: 6172,

Total PFAM families aligned: 327,

Total ORFs with GO annotation: 3077, Total GO terms annotated: 252

Total ORFs with EC annotation: 564, Total EC terms annotated: 57

Alignments and derived results in 'TAB' delimited text files similar to Figure 2c

  1. a Detailed parameters are explained at WebMGA website.