Genbank file specification

National Center for Biotechnology Information , U. Assembly Organizing Genome Coordinates. AGP Specification v2. Contig: a non-redundant sequence formed by joining, based on sequence overlap, one or more smaller sequences.

There should be no gaps in a sequence contig although there may be short runs of Ns due to ambiguous base calls. Scaffold supercontig : a non-redundant sequence formed by joining one or more sequence contigs. The distinction is that no sequence overlap is required to construct the larger sequence. Additional information, such as clone end analysis, can support the relationship.

There can be, and typically there are, gaps in a scaffold. Gap: a sub region within an object where there is no known sequence. You are here: NCBI. External link. Please review our privacy policy. This is the identifier for the object being assembled. The sequencing status of the component. If column 5 not equal to N or U: This is a unique identifier for the sequence component contributing to the object described in column 1.

If column 5 equal to N or U: This column represents the length of the gap. If column 5 not equal to N or U: This column specifies the beginning of the part of the component sequence that contributes to the object in column 1 in component coordinates.

If column 5 equal to N or U: This column specifies the gap type. Accepted values: scaffold: a gap between two sequence contigs in a scaffold superscaffold or ultra-scaffold.

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Open GB file GenBank sequence record. GB file extension - GenBank sequence record. What is gb file? How to open gb files? File type specification: Various data file type. Help how to open: You can open these files using specialized biotechnology software.

In this case the. Commonly used types are:. Some SO types may need to be changed before processing in order to be properly recognized: [a] all gene features should use "gene".

Use "transcript" instead. Feature types that aren't recognized will be automatically dropped and reported in the log file. Feature types that are always ignored so not reported in the log file are:. These are genes that do not encode the expected translation, for example because of internal stop codons.

They can be provided either by including both or neither of them. Specifically [a] and [b], OR just [c]:. Further details are available in the eukaryotic annotation guidelines. These qualifiers do not appear in the flatfile view, so if the GFF3 IDs are meant to be seen in that view, then they should be copied into a 'note' attribute with the appropriate formatting. Multiple values for a qualifier should be provided as a comma-separated list.

Used to specify the location of translation exceptions on a CDS feature where a codon at a specific location on the genome should be translated as an alternative amino acid, such as Sec.

These can also be represented with specific SO feature types in column 3, if they have equivalents in the INSDC class controlled vocabularies. A CDS can only cross a gap of unknown size in introns, not in the actual coding region. If the gap of unknown size is within an exon, then you could split the CDS into two partial CDS features and mRNAs in eukaryotes that abut the gap, with a single gene over the whole locus.

This situation will generate an error. In addition, no feature should begin or end inside a gap. Instead, the feature should abut the gap and be partial. For more information about splitting CDS features, see either the eukaryotic annotation guidelines or the prokaryotic annotation guidelines. Use the command-line program table2asn to combine a template file along with the fasta and annotation. Follow these steps:.