R: Read Annotations from GenBank

getAnnotationsGenBank {ape} | R Documentation

## Read Annotations from GenBank

### Description

This function connects to the GenBank database and reads sequence annotations using accession number(s) given as argument.

### Usage

    getAnnotationsGenBank(access.nb, quiet = TRUE)

### Arguments

`access.nb` | a vector of mode character giving the accession numbers.
`quiet` | a logical value indicating whether to show the progress of the downloads.

### Details

The sequence annotations (a.k.a. feature list) are returned in a data frame with five or six columns: start, end, type, product, others, and gene (the last being optional). This is the same information that can be downloaded from NCBI's Web interface by clicking on ‘Send to:’, ‘File’, and then selecting ‘Feature Table’ under ‘Format’.

A warning is given if some features are incomplete (this information is then dropped from the returned object).

A warning is given if some accession numbers are not found on GenBank.

### Value

On of the followings: (i) a data frame if `access.nb` contains a single accession number; (ii) a list of data frames if `access.nb` contains several accession numbers, the names are set with `access.nb` (if some accession numbers are not found on GenBank, the corresponding entries are set to `NULL`); (iii) `NULL` if all accession numbers are not found on GenBank.

### Author(s)

Emmanuel Paradis

### References

https://www.ncbi.nlm.nih.gov/Sequin/table.html (Note: it seems this URL is broken; 2022-01-03)

### See Also

`read.GenBank`, `read.gff`, `DNAbin`

### Examples

    ## The 8 sequences of tanagers (Ramphocelus):
    ref <- c("U15717", "U15718", "U15719", "U15720",
             "U15721", "U15722", "U15723", "U15724")
    ## Copy/paste or type the following commands if you
    ## want to try them.
    ## Not run:
    annot.rampho <- getAnnotationsGenBank(ref)
    annot.rampho
    ## check all annotations are the same:
    unique(do.call(rbind, annot.rampho)[, -5])

    ## End(Not run)

[Package ape version 5.6-2 Index]