Output dataset¶
Output format overview¶
ProkFunFind will output files with the same prefix.
annot.gff,json,tsv,pklformatted files will be outputed every time. Other files will be reported based on search methods used.
blast.m6¶
The blast output file will only be generated if BLAST was used as part of the search approach.
The BLAST output consists of a tablular blast output table. Column 1 is the protein sequences of genomes; column 2 is the query sequences;
the table format is the BLAST -m 6 format.
GUT_GENOME143137_00182 ecoli_garR 52.203 295 134 3 2 292 3 294 3.80e-104 297
GUT_GENOME143137_00182 cclostridioforme_GarR 51.890 291 139 1 2 291 3 293 6.49e-104 296
GUT_GENOME143137_00419 ecoli_garD 30.208 384 244 7 5 368 122 501 2.39e-52 173
GUT_GENOME143137_00419 cclostridioforme_GarD 33.113 302 195 4 68 368 188 483 5.51e-51 169
GUT_GENOME143137_00648 cclostridioforme_gudA 28.041 296 205 3 82 372 46 338 1.34e-36 126
GUT_GENOME143137_00649 cclostridioforme_gudC 27.273 154 98 4 4 145 8 159 3.05e-06 35.0
GUT_GENOME143137_00650 cclostridioforme_gudB 41.837 490 277 4 13 497 17 503 3.93e-117 345
GUT_GENOME143137_00901 cclostridioforme_gudA 25.200 250 143 6 72 301 46 271 1.78e-12 57.4
GUT_GENOME143137_00903 cclostridioforme_gudB 34.647 482 311 3 17 496 19 498 2.31e-92 281
GUT_GENOME143137_00918 cclostridioforme_GarL 22.378 286 216 4 3 284 6 289 4.03e-21 81.3
hmmtblout¶
The hmmscan output will be generated if hmmscan is used as part of the search approach. This table consists of the targets (profile HMM IDs) in column 1, the gene IDs in column 3, and evalues in column 5.
# --- full sequence ---- --- best 1 domain ---- --- domain number estimation ----
# target name accession query name accession E-value score bias E-value score bias exp reg clu ov env dom rep inc description of target
#------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- ---------------------
HNDD - GCF_000478885.1_00103 - 0.00023 9.8 9.6 0.0039 5.7 9.6 1.9 1 1 0 1 1 1 1 -
HNDD - GCF_000478885.1_00145 - 2.4e-05 13.1 22.2 0.00015 10.4 4.5 2.8 2 2 0 2 2 2 2 -
DEVR - GCF_000478885.1_00174 - 3.6e-07 19.5 0.0 5.8e-07 18.8 0.0 1.2 1 0 0 1 1 1 1 -
annot.gff¶
The annotated gff file provides a summary of the hits to the different ProkFunFind queries along with their genomic locations. The genes that pass the filtering criteria for each search approach are listed in this file. This file can be imported into programs like Geneious for subsequent visualiation and curation.
GUT_GENOME143137_1 ProkFunFind CDS 187675 188575 . - . ID=GUT_GENOME143137_00182;Name=garR;Parent=Cl_0;Target=ecoli_garR 2 294;pct_identity=52.203;evalue=3.8e-104
GUT_GENOME143137_2 ProkFunFind CDS 38455 39622 . + . ID=GUT_GENOME143137_00419;Name=garD;Parent=Cl_0;Target=ecoli_garD 121 501;pct_identity=30.208;evalue=2.39e-52
GUT_GENOME143137_2 ProkFunFind CDS 296187 297321 . + . ID=GUT_GENOME143137_00648;Name=gudA;Parent=Cl_1;Target=cclostridioforme_gudA 45 338;pct_identity=28.041;evalue=1.34e-36
GUT_GENOME143137_2 ProkFunFind CDS 297794 299288 . + . ID=GUT_GENOME143137_00650;Name=gudB;Parent=Cl_1;Target=cclostridioforme_gudB 16 503;pct_identity=41.837;evalue=3.93e-117
GUT_GENOME143137_3 ProkFunFind CDS 239793 240903 . + . ID=GUT_GENOME143137_00901;Name=gudA;Parent=Cl_0;Target=cclostridioforme_gudA 45 271;pct_identity=25.2;evalue=1.78e-12
GUT_GENOME143137_3 ProkFunFind CDS 241398 242916 . + . ID=GUT_GENOME143137_00903;Name=gudB;Parent=Cl_0;Target=cclostridioforme_gudB 18 498;pct_identity=34.647;evalue=2.31e-92
GUT_GENOME143137_3 ProkFunFind CDS 262245 263112 . + . ID=GUT_GENOME143137_00918;Name=garL;Parent=Cl_1;Target=cclostridioforme_GarL 5 289;pct_identity=22.378;evalue=4.03e-21
GUT_GENOME143137_4 ProkFunFind CDS 87018 88551 . - . ID=GUT_GENOME143137_01073;Name=gudB;Parent=Cl_0;Target=cclostridioforme_gudB 18 507;pct_identity=36.531;evalue=6.07e-95
GUT_GENOME143137_4 ProkFunFind CDS 89063 90152 . - . ID=GUT_GENOME143137_01075;Name=gudA;Parent=Cl_0;Target=cclostridioforme_gudA 47 301;pct_identity=26.515;evalue=1.06e-15
GUT_GENOME143137_5 ProkFunFind CDS 36139 37639 . - . ID=GUT_GENOME143137_01304;Name=gudB;Parent=Cl_0;Target=cclostridioforme_gudB 3 480;pct_identity=40.167;evalue=3.42e-120
yaml¶
The yaml file is similar to the input system definition that is provided in the config.yaml file. file with the “genes” added and the “completeness” of each subsystem is added to each component. This file acts an overall summary of the search results.
name: Equol Gene Cluster
components:
- name: Equol Production Pathway
presence: essential
components:
- geneID: DZNR
description: Daidzein reductase
presence: essential
terms:
- id: K00219
method: kofamscan
genes:
- GCF_000478885.1_00950
- GCF_000478885.1_01879
- GCF_000478885.1_02274
...
completeness:
essential: 4
nonessential: 0
essential_presence: 4
nonessential_presence: 0
tsv¶
A tab separated file with three columns, summarizing the hits and gene clusters identified.
Name |
Description |
|---|---|
Gene_Name |
The name of gene |
Cluster_ID |
Genes within the same genomic neighborhood are assigned the same cluster ID. ‘NA’ means that the gene was not found to be in the same neigborhood as any other hits. |
Functions |
What search terms and components a given hit was associated with. |
Gene_Name Cluster_ID Functions
GUT_GENOME143137_00182 GUT_GENOME143137_1:Cl_0 Mucic_and_Saccharic_Acid/garR
GUT_GENOME143137_00419 GUT_GENOME143137_2:Cl_0 Mucic_and_Saccharic_Acid/garD
GUT_GENOME143137_00648 GUT_GENOME143137_2:Cl_1 Mucic_and_Saccharic_Acid/gudA
GUT_GENOME143137_00650 GUT_GENOME143137_2:Cl_1 Mucic_and_Saccharic_Acid/gudB
GUT_GENOME143137_00901 GUT_GENOME143137_3:Cl_0 Mucic_and_Saccharic_Acid/gudA
GUT_GENOME143137_00903 GUT_GENOME143137_3:Cl_0 Mucic_and_Saccharic_Acid/gudB
GUT_GENOME143137_00918 GUT_GENOME143137_3:Cl_1 Mucic_and_Saccharic_Acid/garL
GUT_GENOME143137_01073 GUT_GENOME143137_4:Cl_0 Mucic_and_Saccharic_Acid/gudB
GUT_GENOME143137_01075 GUT_GENOME143137_4:Cl_0 Mucic_and_Saccharic_Acid/gudA
pkl¶
Pickle object of the output Genome object, which can be loaded to python for further analysis. This can be de-serialized using the python pickle module to access and interact with the genome object data.
What to do next?¶
Import the
prefix.annot.gffto genome analysis and visualization software to curate and visualize the results.Re-run
prokfunfind.pyto test other parameters and optimize your search.