external-gene-calls

TXT

A TXT-type anvi’o artifact. This artifact is typically provided by the user for anvi’o to import into its databases, process, and/or use.

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Provided by

anvi-get-sequences-for-gene-calls anvi-script-augustus-output-to-external-gene-calls anvi-script-process-genbank anvi-script-process-genbank-metadata

Required or used by

anvi-gen-contigs-database

Description

By default, anvi’o uses Prodigal for gene calling when the user is generating a contigs-db. Yet, if the user provides an external gene calls file, then anvi’o does not perform gene calling, and uses this file to store the gene information into the new contigs-db.

External gene calls is a user-provided TAB-delimited file that should follow this format:

gene_callers_id contig start stop direction partial call_type source version
1 contig_01 1113 1677 f 0 1 program v1.0
2 contig_01 1698 2142 f 0 1 program v1.0
3 contig_01 2229 3447 f 0 1 program v1.0
4 contig_01 3439 6820 r 0 1 program v1.0
7 contig_01 8496 10350 r 1 1 program v1.0
8 contig_02 306 1650 f 0 1 program v1.0
9 contig_02 1971 3132 f 0 1 program v1.0
10 contig_02 3230 4007 f 0 1 program v1.0
11 contig_02 4080 5202 f 0 1 program v1.0
12 contig_02 5194 5926 f 0 1 program v1.0
13 contig_03 606 2514 f 0 1 program v1.0
14 contig_03 2751 3207 f 0 1 program v1.0
15 contig_03 3219 5616 f 0 1 program v1.0
16 contig_03 5720 6233 f 0 1 program v1.0
(…) (…) (…) (…) (…) (…) (…) (…)  

Please note that while anvi’o will not perform any gene prediction, it will still try to translate DNA sequence found in start-stop positions of each gene using the standard genetic code. You can prevent that by providing your own amino acid sequences by adding an optional column to your external gene calls file, aa_sequence:

gene_callers_id contig start stop direction partial call_type source version aa_sequence
1 contig_01 1113 1677 f 0 1 program v1.0 MAQTTNDIKNGSVLNLDGQLWTVI(…)
2 contig_01 1698 2142 f 0 1 program v1.0 MARSTARKRALNTLYEADEKGQDI(…)
3 contig_01 2229 3447 f 0 1 program v1.0 MNQYDSEAVMFDPQDAVLVLEDGQ(…)
4 contig_01 3439 6820 r 0 1 program v1.0 MPKRTDIKSVMVIGSGPIVIGQAA(…)
7 contig_01 8496 10350 r 1 1 program v1.0 MMSSPSSEEVNAQRSDFGLRLSNS(…)
8 contig_02 306 1650 f 0 1 program v1.0 MADSQHGRLIVLCGPAGVGKGTVL(…)
9 contig_02 1971 3132 f 0 1 program v1.0 MRSAKLMNGRVFAGARALYRAAGV(…)
10 contig_02 3230 4007 f 0 1 program v1.0 MAFGTEPTPTGLADPPIDDLMEHA(…)
11 contig_02 4080 5202 f 0 1 program v1.0 MAELKLISAESVTEGHPDKVCDQI(…)
12 contig_02 5194 5926 f 0 1 program v1.0 MRYPCIMTNEDAEQLALDGLAPRK(…)
13 contig_03 606 2514 f 0 1 program v1.0 MTLTLRMEKRMKGWPGEPQMEYDV(…)
14 contig_03 2751 3207 f 0 1 program v1.0 MLKVLFAGTPDVAVPSLKLLAQDT(…)
15 contig_03 3219 5616 f 0 1 program v1.0 MLEQETPNIASMASLPTLSAPGLL(…)
16 contig_03 5720 6233 f 0 1 program v1.0 MLESEVDMNDHDEETLASLQQAND(…)
(…) (…) (…) (…) (…) (…) (…) (…) (…)  

Explicitly defining amino acid sequences could be particularly useful when working with eukaryotic genomes, and/or genomes that use non-standard genetic code. Sections below discuss specific information about columns of this file.

Gene start/stop positions

Anvi’o follows the convention of string indexing and splicing that is identical to the way one does it in Python or C. This means that the index of the first nucleotide in any contig should be 0. In other words, for a gene call that starts at the position xth position and ends at position yth position, we start counting from x-1, and not from x (but we still end at y). The start and stop positions in the input file should comply with this criterion. Here is an example gene in a contig:

                 1         2         3
nt pos: 12345678901234567890123456789012 (...)
contig: NNNATGNNNNNNNNNNNNNNNNNTAGAAAAAA (...)
           |______ gene X _______|

The start and stop positions in the input file for this gene should be 3 and 26, respectively. Which means, if you are trying to generate an external gene calls file from gene calls produced by a gene caller that reports start/stop positions starting with the index of 1 rather than 0, you basically need to subtract one from the start position of every gene call for a matching anvi’o external gene calls file.

Gene start and stop positions do not care about the direction of the gene as they simply address how the gene sequence should be sliced out from a longer sequence. Whether a gene is forward or reverse is defined in the column direction.

You can read the previous discussions regarding this behavior in this issue). Thanks for your patience!

Call type

This is a feature added after anvi’o v6.2. If you are using anvi’o v6.2 or earlier, please remove call_type column from your external gene calls file.

The column call_type declares the nature of the call. It can take one of the following three integer values:

  • 1, indicates that the gene call is for a CODING gene. For gene calls marked as CODING genes, anvi’o will try to predict the proper coding frame when anvi-gen-contigs-database is run using Markov models trained on a large number of protein sequences and was first described in this pull request. This is the default behavior for CODING sequences regardless of whether the gene call is partial or not. However, there are two ways the user can change this: (1) by providing an amino acid sequence for the call in the aa_sequence column or (2) by asking anvi-gen-contigs-database to --skip-predict-frame.

  • 2, indicates that the gene call is for a NONCODING gene. This is used for non-coding RNAs (transfer RNAs or ribosomal RNAs). For gene calls marked as NONCODING, anvi’o will not attempt to predict an amino acid sequence (nor it will tolerate entries in the aa_sequence column).

  • 3, indicates that the gene call is for an UNKNOWN genomic region. This is currently reserved for experimental purposes.

Edit this file to update this information.

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