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At the annual meeting of the International Nucleotide Sequence Databases (INSD), DDBJ, EMBL and GenBank agreed to adopt two new qualifiers to describe the evidence for features in sequence records. These are "/experimental=text" and "/inference=TYPE:text", where 'TYPE' is from a select list and 'text' is structured text (described below). These new qualifiers replace "evidence=experimental" and "evidence=non-experimental", respectively, which will no longer be supported.
/experiment
Definition: a brief description of the nature of the experimental evidence that supports the feature identification or assignment.
Value format: "text"
- Examples:
- /experiment="Northern blot"
/experiment="heterologous expression system of Xenopus laevis oocytes"
Comment: detailed experimental details should not be included, and would normally be found in the cited publications.
/inference
Definition: a structured description of non-experimental evidence that supports the feature identification or assignment.
Value format: "TYPE[ (same species)][:EVIDENCE_BASIS]"
where TYPE is restricted to one of the following 11 choices:
- /inference="similar to sequence"
- /inference="similar to AA sequence"
/inference="similar to DNA sequence"
/inference="similar to RNA sequence"
-
- /inference="similar to RNA sequence, mRNA"
/inference="similar to RNA sequence, EST"
/inference="similar to RNA sequence, other RNA"
- /inference="profile"
- /inference="nucleotide motif"
/inference="protein motif"
/inference="ab initio prediction"
The optional text "(same species)" can be included when the inference comes from the same species as the entry.
The "EVIDENCE_BASIS" is text that gives a reference to a database entry (including accession and version) or an algorithm (including version). The accession.version number of a database record and the version number of an algorithm are separated from the database or algorithm name by a colon, as seen in the examples.
- Examples:
- /inference="similar to DNA sequence:INSD:AY411252.1"
/inference="similar to RNA sequence, mRNA:RefSeq:NM_000041.2"
/inference="similar to DNA sequence (same species):INSD:AACN010222672.1"
/inference="profile:tRNAscan:2.1"
/inference="protein motif:InterPro:IPR001900"
/inference="ab initio prediction:Genscan:2.0"
Several things to note about /inference are:
- When citing a GenBank record, use INSD (International Sequence Database).
- When citing a RefSeq record (recognized by the underscore between the letters and the digits), use RefSeq.
- Include the version of the algorithm that was used, and separate the version from the algorithm name with a colon, eg Genscan:2.0.
Old evidence qualifiers
Previous instances of "evidence=experimental" and "evidence=non-experimental" will be automatically converted to /experiment="experimental evidence, no additional details recorded"
/inference="non-experimental evidence, no additional details recorded"
but these phrases may not be used on new records.
How to add the new qualifiers to your genome submissions
New versions of tbl2asn and Sequin support these new qualifiers
To use the new qualifiers in tbl2asn, include them in the .tbl file as you do other qualifiers. Example .tbl file:
In this example the first CDS is predicted by Genscan 2.0, the second CDS was identified by its similarity to EST H22345.1 from the same species, the third CDS was identified because it's similar to GenBank (INSD) record AY123456.2 and by its InterPro domain IPR001900, and the fourth CDS has experimental expression evidence.
>Feature ExampleSeq
1 100 gene
locus_tag Test_0001
1 100 CDS
product Test_0001
protein_id gnl|center_name|Test_0001
inference ab initio prediction:Genscan:2.0
200 300 gene
locus_tag Test_0002
200 300 CDS
product Test_0002
protein_id gnl|center_name|Test_0002
inference similar to RNA sequence, EST (same species):INSD:H22345.1
400 500 gene
locus_tag Test_0003
400 500 CDS
product Test_0003
protein_id gnl|center_name|Test_0003
inference similar to RNA sequence, mRNA:INSD:AY123456.2
inference protein motif:InterPro:IPR001900
600 700 gene
locus_tag Test_0004
600 700 CDS
product Test_0004
protein_id gnl|center_name|Test_0004
experiment expression of GST fusion protein
The resulting flatfile looks like this:
gene 1..100
/locus_tag="Test_0001"
CDS 1..100
/locus_tag="Test_0001"
/inference="ab initio prediction:Genscan:2.0"
/codon_start=1
/product="Test_0001"
/translation="M...."
gene 200..300
/locus_tag="Test_0002"
CDS 200..300
/locus_tag="Test_0002"
/inference="similar to RNA sequence, EST (same
species):INSD:H223456.1"
/codon_start=1
/product="Test_0002"
/translation="M...."
gene 400..500
/locus_tag="Test_0003"
CDS 400..500
/locus_tag="Test_0003"
/inference="protein motif:InterPro:IPR001900"
/inference="similar to RNA sequence, mRNA:INSD:AY123456.2"
/codon_start=1
/product="Test_0003"
/translation="M...."
gene 600..700
/locus_tag="Test_0004"
CDS 600..700
/locus_tag="Test_0004"
/experiment="expression of GST fusion protein"
/codon_start=1
/product="Test_0004"
/translation="M...."
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