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KofamScan

KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool. Online version is available on https://www.genome.jp/tools/kofamkoala/ .

Requirements

  • Linux
  • Ruby >= 2.4
  • HMMER >= 3.1
  • GNU Parallel

Usage

  1. Download KOfam database from ftp://ftp.genome.jp/pub/db/kofam/ and decompress it. You will get profile HMMs in profiles/ directory and ko_list.
  2. Create config.yml in the same directory as exec_annotation script. See below for details.
  3. Execute exec_annotation.
$ ./exec_annotation -o result.txt query.fasta

Query file

A query file is a FASTA file with one or more amino acid sequences. You cannot use nucleotide sequences. Each sequence must have a unique name. A name of a sequence is a string between the header symbol (">") and the first blank character (whitespace, tab, line break, etc.). Do not put a whitespace right after ">".

Profiles

Specify the path of the profile database you downloaded by giving --profile option to the command or writing it to config.yml. The path can be a directory, .hmm file, or .hal file. If it is a directory, .hmm files in the directory will be used. If a .hmm file, only the file will be used. If a .hal file, files listed in the .hal file will be used. File paths in a .hal file are either absolute or relative to the directory of the file. Lines start with # are ignored.

KOfam has prokaryote.hal and eukaryote.hal in profiles directory. They are lists of profiles excluding eukaryote- and prokaryote-specific KOs respectively. If you are interested in only several KOs, you can make your original .hal file and use it as a database. It will reduce computation time.

Options

  • -o FILE
    • The result are output to FILE. It defaults to stdout.
  • -p, --profile=PROFILE
    • Use PROFILE as a profile database. See Profiles
  • -k, --ko-list=FILE
    • Use FILE as a KO list.
  • --cpu=N
    • Set the number of hmmsearch processes started simultaneously to N. It defaults to 1 unless it is set in config.yml.
  • -c FILE
    • Use FILE as a config file instead of config.yml in the same directory as exec_annotation.
  • --tmp-dir=DIR
    • Use DIR as a temporary directory where hmmsearch results are. It will be created if not exist. It defaults to ./tmp.
  • -E, --e-value=VALUE
    • Require E-value to be smaller than or equal to VALUE. If not, an asterisk will not be added in detail format or the hit will not be reported in other formats.
  • -T, --threshold-scale=VALUE
    • The score thresholds are multiplied by VALUE. For example, with -T2 option, the thresholds become twice as strict.
  • -f, --format=FORMAT
    • Set the format of the output to FORMAT. Three formats below are available.
    • detail
      • Default format. Gene name, assigned K number, threshold of the KO, hmmsearch score and E-value, and the definition of KO are shown. In addition, an asterisk '*' is added to the head of the line if the score is higher than the threshold.
    • detail-tsv
      • Tab separated values for detail format.
    • mapper
      • Format which can be used for KEGG Mapper input. It includes a gene name and an assigned K number separated by a tab. Here, an assigned K number represents a hit with score above the predefined threshold. Note that for some KOs, predefined score thresholds are not available when they are represented by a very few number of sequences in KEGG GENES.
    • mapper-oneline
      • Similar to mapper, but when more than one KO are assigned to a gene, all assigned KO are shown in one line separated by tabs.
  • --[no-]report-unannotated
    • With --report-unannotated option, gene names are shown even when no KO is assigned (default when --format=mapper(-oneline)). With --no-report-unannotated such genes are not shown at all (default when --format=detail).
  • --create-alignment
    • hmmsearch's normal outputs per profile are stored in the temporary directory. In addition, domain information and alignments in the outputs will be rearranged per query.
    • Not compatible with --reannotation
  • -r, --reannotation
    • Skip hmmsearch and assume that hmmsearch outputs are already in the temporary directory. This will help you to make an output in a different format or redo annotation changing thresholds.
    • Not compatible with --create-alignment
  • -h, --help
    • Show brief help message.

config.yml

The following variables can be set by config.yml.

  • profile
    • Path to KOfam profiles.
    • --profile option takes precedence.
  • ko_list
    • Path to the KO list of KOfam.
    • --ko-list option takes precedence.
  • cpu
    • Number of hmmsearch processes started simultaneously.
    • --cpu option takes precedence.
  • hmmsearch
    • Path to hmmsearch executable. If not given, it will be searched for PATH.
  • parallel
    • Path to parallel executable. If not given, it will be searched for PATH.

License

This software is released under the MIT License.