getAnnotationsGenBank: Read Annotations from GenBank

In ape: Analyses of Phylogenetics and Evolution

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)

ape documentation built on May 29, 2024, 10:50 a.m.