functions-txt

TXT

A TXT-type anvi’o artifact. This artifact can be generated, used, and/or exported by anvi’o. It can also be provided by the user for anvi’o to import into its databases, process, and/or use.

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Provided by

anvi-export-functions anvi-search-functions anvi-script-get-hmm-hits-per-gene-call anvi-script-process-genbank anvi-script-process-genbank-metadata anvi-script-transpose-matrix

Required or used by

anvi-import-functions anvi-script-transpose-matrix

Description

This artifact is a TAB-delimited file that associates genes and functions.

The user can generate this file to import gene functions into a contigs-db via anvi-import-functions or can acquire this file by recovering it from a contigs-db via anvi-export-functions. It is also the output of anvi-search-functions which searches for specific terms in your functional annotations.

In general, this is the simplest way to get gene functions into anvi’o, and all downstream analyses, including pangenomics. For other ways to get gene functions into anvi’o you can take a look at this page.

Simple matrix file format

The TAB-delimited file for this artifact has five columns:

  1. gene_callers_id: The gene caller ID recognized by anvi’o (see the note below).
  2. source: The name of the functional annotation source (i.e., the database that you got this function data from).
  3. accession: A unique accession id per function, better if a single word.
  4. function: Full name / description of the function.
  5. e_value: The significance score of this annotation, where zero is maximum significance. This information may be used by anvi’o in operations that require filtering of functions based on their significance.

Through this file format you can import functions from any source into anvi’o, whether those sources are commonly used programs to annotate genes with functions or your ad hoc manual curations for genes of interest. But please note while there are many ways to have your genes annotated with functions, there is only one way to make sure the gene caller ids anvi’o knows will match perfectly to the gene caller ids in your input file. The best way to ensure that linkage is to export your gene DNA or amino acid sequences for your an contigs-db using the anvi’o program anvi-get-sequences-for-gene-calls.

An example matrix

Here is an example file that matches to this format that can be used with anvi-import-functions to import functions into a contigs-db:

gene_callers_id source accession function e_value
1 Pfam PF01132 Elongation factor P (EF-P) OB domain 4e-23
1 Pfam PF08207 Elongation factor P (EF-P) KOW-like domain 3e-25
1 TIGRFAM TIGR00038 efp: translation elongation factor P 1.5e-75
2 Pfam PF01029 NusB family 2.5e-30
2 TIGRFAM TIGR01951 nusB: transcription antitermination factor NusB 1.5e-36
3 Pfam PF00117 Glutamine amidotransferase class-I 2e-36
3 Pfam PF00988 Carbamoyl-phosphate synthase small chain, CPSase domain 1.2e-48
3 TIGRFAM TIGR01368 CPSaseIIsmall: carbamoyl-phosphate synthase, small subunit 1.5e-132
4 Pfam PF02787 Carbamoyl-phosphate synthetase large chain, oligomerisation domain 1.4e-31
4 TIGRFAM TIGR01369 CPSaseII_lrg: carbamoyl-phosphate synthase, large subunit 0
5 TIGRFAM TIGR02127 pyrF_sub2: orotidine 5’-phosphate decarboxylase 1.9e-59
6 Pfam PF00625 Guanylate kinase 5.7e-39
6 TIGRFAM TIGR03263 guanyl_kin: guanylate kinase 3.5e-62
8 Pfam PF01192 RNA polymerase Rpb6 4.9e-13
8 TIGRFAM TIGR00690 rpoZ: DNA-directed RNA polymerase, omega subunit 1.7e-20
9 TIGRFAM TIGR01034 metK: methionine adenosyltransferase 2.5e-169
11 Pfam PF13419 Haloacid dehalogenase-like hydrolase 2.8e-27
11 TIGRFAM TIGR01509 HAD-SF-IA-v3: HAD hydrolase, family IA, variant 3 1.2e-11
12 Pfam PF00551 Formyl transferase 1.4e-34
12 TIGRFAM TIGR00460 fmt: methionyl-tRNA formyltransferase 2.9e-70
13 Pfam PF12710 haloacid dehalogenase-like hydrolase 2.3e-14
13 TIGRFAM TIGR00338 serB: phosphoserine phosphatase SerB 4.9e-76
13 TIGRFAM TIGR01488 HAD-SF-IB: HAD phosphoserine phosphatase-like hydrolase, family IB 6e-29
14 Pfam PF00004 ATPase family associated with various cellular activities (AAA) 7.7e-45
14 Pfam PF16450 Proteasomal ATPase OB/ID domain 1.8e-34
14 TIGRFAM TIGR03689 pup_AAA: proteasome ATPase 1e-206
(…) (…) (…) (…) (…)

Please note that,

  • Not every gene call has to be present in the matrix,

  • It is OK if there are multiple annotations from the same source for a given gene call,

  • It is OK if a give gene is annotated only by a single source.

  • If the accession information is not available to you, it is OK to leave it blank (but it will prevent you from being able to use some toys, such as functional enrichment analyses later for pangenomes).

  • If you have no e-values associated with your annotations, it is OK to put 0 for every entry (you should make sure you keep this in mind for your downstream analyses that may require filtering of weak hits).

  • If there are multiple annotations from a single source for a single gene call, anvi’o uses e-values in this file to use only the most significant one to show in interfaces.

Edit this file to update this information.

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